From 47e40fe47d5f0c839203a49734bd64377b40e629 Mon Sep 17 00:00:00 2001 From: Niels van der Velden Date: Mon, 2 Sep 2024 17:52:15 -0300 Subject: [PATCH] Update documentation to set width for rendering to PDF --- docs/articles/geneviewer.html | 7 +++++-- docs/pkgdown.yml | 2 +- docs/search.json | 2 +- 3 files changed, 7 insertions(+), 4 deletions(-) diff --git a/docs/articles/geneviewer.html b/docs/articles/geneviewer.html index e2f9626..4262a41 100644 --- a/docs/articles/geneviewer.html +++ b/docs/articles/geneviewer.html @@ -1656,7 +1656,10 @@

Saving Plots
 library(webshot2)
 
@@ -1665,7 +1668,7 @@ 
Saving PlotsGC_chart(ophA_clusters, 
            group = "class", 
            cluster = "cluster",
-           width = "400px",
+           width = "400px", # Essential to prevent misalignment of gene links
            height = "250px")
 
 # Save plot to temp.html file
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 5a89a46..0797b4c 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
   LoadGFF: LoadGFF.html
   MUMMER: MUMMER.html
   Transcripts: Transcripts.html
-last_built: 2024-08-31T21:01Z
+last_built: 2024-09-02T20:47Z
 urls:
   reference: https://nvelden.github.io/geneviewer/reference
   article: https://nvelden.github.io/geneviewer/articles
diff --git a/docs/search.json b/docs/search.json
index 5b4aabf..de608eb 100644
--- a/docs/search.json
+++ b/docs/search.json
@@ -1 +1 @@
-[{"path":"https://nvelden.github.io/geneviewer/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2023 geneviewer authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/BLASTP.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Cluster comparison using BlastP","text":"tutorial describes can use geneviewer identify visualize homologous genes across clusters performing BlastP alignment. demonstrate use GenBank file contains genes involved biosynthesis erythromycin Saccharopolyspora erythraea compare several homologous clusters different species identified using antiSMASH. guidance importing clusters GenBank files, please refer guide.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/BLASTP.html","id":"materials","dir":"Articles","previous_headings":"","what":"Materials","title":"Cluster comparison using BlastP","text":".gbk files additional gene info can downloaded geneviewer-tutorials repository. visualization, geneviewer package required. Sequence alignment performed using Biostrings pwalign packages can downloaded Bioconductor. Optionally, parallel package can utilized increase processing times.","code":"devtools::install_github(\"nvelden/geneviewer\") BiocManager::install(\"Biostrings\") BiocManager::install(\"pwalign\") # Optional but recommended for speeding up processing install.packages(\"parallel\")   library(geneviewer) library(Biostrings) library(pwalign) library(parallel)"},{"path":"https://nvelden.github.io/geneviewer/articles/BLASTP.html","id":"loading-cluster-information","dir":"Articles","previous_headings":"","what":"Loading cluster information","title":"Cluster comparison using BlastP","text":"cluster information needed run BlastP can loaded directly .gbk files pointing folder path contains files running protein_blast() function. Alternatively, protein blast can performed using data.frame contains start, end, strand, translation well unique identifier gene cluster shown .","code":"# change the path to the folder where the .gbk files are saved folder_path <- \"~/path/to/folder/\""},{"path":"https://nvelden.github.io/geneviewer/articles/BLASTP.html","id":"run-blastp","dir":"Articles","previous_headings":"","what":"Run BlastP","title":"Cluster comparison using BlastP","text":"tutorial, directly input folder path protein_blast() function load data. ’ll select BGC0000055 query cluster conduct BlastP analysis find homologous clusters. use 30 minimum identity threshold. Performing BlastP analysis dataset can take several minutes set parallel processing TRUE. smaller datasets parallel package installed, set parallel processing FALSE. running BlastP, dataset contain three additional columns. colums : BlastP: Indicates top BlastP match found within query cluster, characterized unique protein id. identity: percentage identity BlastP hit. similarity: percentage similarity BlastP hit. score: Synteny score clusters based used antiSMASH/MultiGeneBlast. can visualize results using geneviewer. graph clusters ordered based synteny score. genes colored BlasP hit found query cluster. Genes remain uncolored significant homologous. hoovering genes one can see percentage identity similarity.","code":"BlastP_results <- geneviewer::protein_blast(   folder_path,   query = \"BGC0000055\",   id = \"protein_id\", # Name of column containing gene identifiers.    cluster = \"cluster\", # Name of column containing cluster identifiers.    identity = 30,   parallel = TRUE ) GC_chart(   data = BlastP_results,   cluster = \"cluster\",   strand = \"strand\",   group = \"BlastP\",   height = \"400px\" ) %>% GC_clusterLabel() %>% GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/BLASTP.html","id":"color-by-gene-function","dir":"Articles","previous_headings":"","what":"Color by gene function","title":"Cluster comparison using BlastP","text":"Rather assigning colors genes based BlastP matches, can color gene function. can bind extra gene information specific query cluster BGC0000055_info.csv file. executing left_join() operation BlastP_results dataset BlastP field, can add extra information BlastP results. can now use Function category color genes. ’ll also add gene names, links, BlastP identity values cluster information. Alternatively, GC_links() function allows highlighting connections specific genes utilizing value1 value2 parameters. gain insights cluster sizes, can adjust axis_type range. additional styling coloring options, refer GC_links() GC_scale documentation.","code":"# change the path to the folder where the .gbk files are saved BGC0000055_info <- \"~/path/to/folder/BGC0000055_info.csv\" BlastP_results_functions <- left_join(BlastP_results, BGC0000055_info, by = dplyr::join_by(BlastP == protein_id ) ) GC_chart(   data = BlastP_results_functions,   cluster = \"cluster\",   group = \"Functions\",   strand = \"strand\",   height = \"600px\" ) %>% GC_labels(label = \"Gene\", cluster = 1) %>%  GC_links(group = \"BlastP\",  measure = \"identity\") %>%   GC_clusterLabel() %>% GC_legend(TRUE) GC_chart(   data = BlastP_results_functions,   cluster = \"cluster\",   group = \"Functions\",   strand = \"strand\",   height = \"600px\" ) %>% GC_labels(label = \"Gene\", cluster = 1) %>%  GC_scale(axis_type = \"range\") %>% GC_links(group = \"Gene\",            value1 = c(\"eryAI\", \"eryAII\", \"eryAIII\"),           value2 = c(\"eryAI\", \"eryAII\", \"eryAIII\"),           use_group_colors = TRUE          ) %>%   GC_clusterLabel() %>% GC_legend(TRUE)"},{"path":"https://nvelden.github.io/geneviewer/articles/Examples.html","id":"e-coli-lac-operon","dir":"Articles","previous_headings":"","what":"E.coli Lac operon","title":"Example charts","text":"","code":"lacZ_operon <- data.frame(   start = c(361249, 361926, 363231, 366428),    end = c(361860, 363179, 366305, 367510),    Gene_symbol = c(\"lacA\", \"lacY\", \"lacZ\", \"lacI\"),    Strand = c(\"minus\", \"minus\", \"minus\", \"minus\"),    NCBI_Gene_ID = as.character(c(945674, 949083, 945006, 945007)),    Description = c(\"galactoside O-acetyltransferase\",                    \"lactose permease\", \"beta-galactosidase\",                    \"DNA-binding transcriptional repressor LacI\") )  GC_chart(lacZ_operon, group = \"Gene_symbol\", height = \"140px\") %>%   GC_labels() %>%   GC_scaleBar(title = \"0.2 kb\", scaleBarUnit = 200, y=30) %>%   GC_tooltip(     formatter = \"     ID:<\/b> {NCBI_Gene_ID}
     Description:<\/b> {Description}
     Start:<\/b> {start}
     End:<\/b> {end}\",   ) %>%   GC_clusterFooter(     align = \"center\",     y = -30,     subtitle = \"Escherichia coli<\/i> str. K-12 substr. MG1655\"    ) %>%   GC_coordinates(     rotate = 0,     tickValuesBottom = c(min(lacZ_operon$start), max(lacZ_operon$end)),     textStyle = list(fontSize = \"10px\", x = -2.2, y = 1.2),     tickStyle = list(lineLength = 10)     ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/Examples.html","id":"omphalotin-gene-clusters","dir":"Articles","previous_headings":"","what":"Omphalotin gene clusters","title":"Example charts","text":"","code":"GC_chart(ophA_clusters,             start = \"start\",            end = \"end\",            group = \"class\",            cluster = \"cluster\") %>%   GC_clusterFooter(     title = c(\"Omphalotus olearius<\/i>\", \"Dendrothele bispora<\/i>\"),      subtitle = c(\"Locus: 2,522 - 21,484\", \"Locus: 19,236 - 43,005\"),     align = \"left\",     x = 50) %>%   GC_legend(position = \"top\") %>%   GC_labels(label = \"name\") %>%   GC_scaleBar(y = 20) %>%   GC_scale(cluster = 1,  scale_breaks = TRUE, hidden = TRUE) %>%   GC_scale(cluster = 2, reverse = TRUE, hidden = TRUE) %>%   GC_tooltip(     formatter = \"Gene:<\/b> {name}
 Start:<\/b> {start}
end:<\/b> {end}\"   )"},{"path":"https://nvelden.github.io/geneviewer/articles/Examples.html","id":"h--sapiens-hox-genes-using-biomart","dir":"Articles","previous_headings":"","what":"H. sapiens Hox genes using biomaRt","title":"Example charts","text":"","code":"# Get HOX gene positions  library(biomaRt)  ensembl <- useMart(\"ensembl\", dataset = \"hsapiens_gene_ensembl\")  hox_gene_sets <- list(   HOXA = c(\"HOXA1\", \"HOXA2\", \"HOXA3\", \"HOXA4\", \"HOXA5\", \"HOXA6\", \"HOXA7\", \"HOXA9\", \"HOXA10\", \"HOXA11\", \"HOXA13\"),   HOXB = c(\"HOXB1\", \"HOXB2\", \"HOXB3\", \"HOXB4\", \"HOXB5\", \"HOXB6\", \"HOXB7\", \"HOXB8\", \"HOXB9\", \"HOXB13\"),   HOXC = c(\"HOXC4\", \"HOXC5\", \"HOXC6\", \"HOXC8\", \"HOXC9\", \"HOXC10\", \"HOXC11\", \"HOXC12\", \"HOXC13\"),   HOXD = c(\"HOXD1\", \"HOXD3\", \"HOXD4\", \"HOXD8\", \"HOXD9\", \"HOXD10\", \"HOXD11\", \"HOXD12\", \"HOXD13\") )  get_gene_positions <- function(gene_list, cluster_name) {    result <- getBM(attributes = c('hgnc_symbol', 'chromosome_name', 'strand', 'start_position', 'end_position'),                   filters = 'hgnc_symbol',                   values = gene_list,                   mart = ensembl)   transform(result, cluster = cluster_name) }  # Apply get_gene_positions to each gene set hox_gene_positions <- base::lapply(names(hox_gene_sets), function(cluster_name) {   get_gene_positions(hox_gene_sets[[cluster_name]], cluster_name) })  # Combine the results into a single data frame combined_hox_genes <- do.call(rbind, hox_gene_positions)  # Add gene names combined_hox_genes$name <- paste0(substr(combined_hox_genes$hgnc_symbol, 1, 3), substr(combined_hox_genes$hgnc_symbol, 5, nchar(combined_hox_genes$hgnc_symbol))) GC_chart(   combined_hox_genes,   start = \"start_position\",   end = \"end_position\",   group = \"cluster\",   height = \"400px\",   strand = \"strand\",   cluster = \"cluster\") %>%   GC_sequence(y=45) %>%   GC_legend(FALSE) %>%   GC_clusterLabel(title = unique(human_hox_genes$cluster)) %>%   GC_genes(     marker = \"boxarrow\",     markerHeight = 10,     arrowheadHeight = 10,     arrowheadWidth = 3   ) %>%    GC_labels(label = \"name\", fontSize = \"10px\", adjustLabels = FALSE) %>%   GC_labels(cluster = 2, label = \"name\", itemStyle = list(list(index = 5, x = -4))) %>%   GC_scale(     cluster = c(1,2),     hidden = TRUE,     reverse = TRUE   ) %>%   GC_cluster(prevent_gene_overlap = TRUE, overlap_spacing=20)"},{"path":"https://nvelden.github.io/geneviewer/articles/Examples.html","id":"brca1-splice-variants","dir":"Articles","previous_headings":"","what":"BRCA1 splice variants","title":"Example charts","text":"","code":"GC_chart(BRCA1_splice_variants, height = \"600px\") %>%   GC_transcript(     transcript = \"ensembl_transcript_id\",      strand = \"strand\",      type = \"type\",   ) %>%   GC_clusterTitle(     title = unique(BRCA1_splice_variants$ensembl_transcript_id),     titleFont = list(       fontSize = \"12px\"     )   ) %>%   GC_clusterFooter(     title = c(\"0.8%\", \"0.1%\", \"0.07%\", \"0.02%\", \"0.01%\"),     align = \"center\"   )"},{"path":"https://nvelden.github.io/geneviewer/articles/Examples.html","id":"saccharopolyspora-erythraea-erythromycin","dir":"Articles","previous_headings":"","what":"Saccharopolyspora erythraea Erythromycin","title":"Example charts","text":"","code":"colors <- list(   \"Tailoring (Hydroxylation)\" = \"#d62728\",    \"Precursor biosynthesis\" = \"#2ca02c\",   \"Tailoring (Glycosylation)\" = \"#e6b0aa\",    \"Scaffold biosynthesis\" = \"#9467bd\",    \"Tailoring (Methylation)\" = \"#8b0000\",    \"Activation / processing\" = \"#1f77b4\",    \"Resistance / immunity\" = \"#f7dc6f\" ,   \"Other\" = \"#808080\" )  GC_chart(erythromycin_cluster,           start = \"Start\",          end = \"End\",          height = \"160px\",          group = \"Functions\") %>%   GC_title(     title = \"Erythromycin A biosynthetic gene cluster from Saccharopolyspora erythraea<\/i>\",     height = 40,     align = \"left\"     ) %>%   GC_genes(     marker = \"boxarrow\",     marker_size = \"small\"   ) %>%   GC_tooltip(     formatter = \"{Identifiers}<\/b>                  
{Product}                  
{start} - {end}({Strand})\"    ) %>%   GC_scale(     start = 778000,     end = 832000,     ticksCount = 8   ) %>%   GC_legend(     legendTextOptions = list(fontSize = \"12px\"),     order = c(setdiff(sort(erythromycin_cluster$Functions), \"Other\"), \"Other\")          ) %>%   GC_color(customColors = colors)"},{"path":"https://nvelden.github.io/geneviewer/articles/Examples.html","id":"saccharopolyspora-erythraea-erythromycin-blastp","dir":"Articles","previous_headings":"","what":"Saccharopolyspora erythraea Erythromycin BlastP","title":"Example charts","text":"","code":"### Erythromycin BlastP GC_chart(erythromycin_BlastP,           cluster = \"cluster\",          strand = \"strand\",          group = \"Functions\",          height = 700) %>%   GC_title(     title = \"BlastP Results\"   ) %>%   GC_labels(\"Gene\", cluster = 1) %>%   GC_links(group = \"Gene\",             show_links = FALSE,            color_bar = FALSE,            labelStyle = list(fontSize = \"10px\")            ) %>%   GC_clusterLabel() library(dplyr) ### Erythromycin BlastP GC_chart(erythromycin_BlastP %>% dplyr::filter(cluster %in% c(\"BGC0000055\", \"BGC0000054\")),           cluster = \"cluster\",          strand = \"strand\",          group = \"BlastP\",          height = 250) %>%   GC_labels(\"Gene\", cluster = 1) %>%   GC_genes(marker_size = \"small\", marker = \"rbox\", markerHeight = 15) %>%   GC_links(group = \"BlastP\",             label = FALSE,            color_bar = FALSE            ) %>%   GC_clusterLabel() %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadFastaFiles.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Loading Gene Clusters From FASTA Files","text":"tutorial demonstrates creating gene cluster visualizations FASTA files using geneviewer. guidance importing clusters GenBank files see: link. geneviewer parses FASTA headers extract key-value pairs, denoted =. instance, FASTA header identifies ‘protein’ ‘putative phosphoenolpyruvate synthase’ similarly processes pairs. ‘location’ tag crucial allows extraction ‘start’, ‘end’, ‘strand’ information gene.","code":">lcl|HQ3864.1_prot_ADX475.1_1 protein=putative phosphoenolpyruvate synthase protein_id=ADX66475.1 location=complement(<1..2247) gbkey=CDS MRATGLVRGRAAKRFGRAGGAGDAIGQCRATGHDCLGGSAMIEQYVWDLHEVDETQVAVVGGKGAHLGGL SRIEGIRVPAGFCVTTDAFRRIMAEAPSIDDGLDQLSRLNPDDREAIRTLSAQIRRTIEGIAIPGDLAAA ITRALARLGEHAACAVRSSATAEDLPTASFAGQQDTYLNVVGPTAILQHVSRCWASLFTERAVTYRQRNG"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadFastaFiles.html","id":"materials","dir":"Articles","previous_headings":"","what":"Materials","title":"Loading Gene Clusters From FASTA Files","text":"FASTA files uses tutorial originally downloaded NCBI website can downloaded directly geneviewer-tutorials repository.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/LoadFastaFiles.html","id":"loading-fasta-files","dir":"Articles","previous_headings":"","what":"Loading FASTA files","title":"Loading Gene Clusters From FASTA Files","text":"example FASTA files used tutorial different organism holds genes cluster produces polyene antifungal agent. Download files place folder. can read files R using read_fasta function geneviewer. function uses Biostrings library need load well. function parse FASTA headers create data.frame extracted information. set sequence FALSE since need sequences create cluster visualization. data.frame holds protein IDs, start, end strand information gene. addition cluster column tells us file gene coming.","code":"library(geneviewer) # if (!require(\"BiocManager\", quietly = TRUE)) #     install.packages(\"BiocManager\") #  # BiocManager::install(\"Biostrings\") library(Biostrings)  # change the path to the folder where you have saved the file file_path <- \"~/path/to/folder/\" fasta_df <- read_fasta(file_path, sequence = FALSE) View(fasta_df) # Inspect the data.frame in Rstudio"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadFastaFiles.html","id":"cluster-visualization","dir":"Articles","previous_headings":"","what":"Cluster Visualization","title":"Loading Gene Clusters From FASTA Files","text":"Using data.frame created FASTA files can now easily make cluster visualization.","code":"# Make the cluster chart chart <- GC_chart(   fasta_df,   start = \"start\",   end = \"end\",   strand = \"strand\",   cluster = \"cluster\",   height = \"400px\" ) %>%    GC_clusterLabel(unique(fasta_df$cluster)) chart"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadFastaFiles.html","id":"uniprot-keywords","dir":"Articles","previous_headings":"","what":"Uniprot Keywords","title":"Loading Gene Clusters From FASTA Files","text":"can get additional information gene using Uniprot.ws package. make connection database using UniProt.ws function. Using keytypes() can see keys can use query database columns() can see different fields can get return. gene IDs EMBL-GenBank-DDBJ_CDS identifiers. tutorial want return keywords associated gene can use group genes based function. return data.frame original identifiers, uniprotIDs keywords associated gene. now bit data wrangling help dplyr package performing following steps: split keywords gene “;” Count occurrence keyword gene keep highest occurring keyword Replace keyword less 10 occurrences “” Bind keywords fasta_df protein ID Replace genes without keyword Select columns need visualization can now make visual use keywords group genes. alter order legend alphabetical order group placed last finally customize tooltip also show protein Id hoover. customization options like setting title, altering colors adding gene links much see Get Started Examples.","code":"library(UniProt.ws)  up <- UniProt.ws::UniProt.ws()  keytypes(up) columns(up)  keywords <- UniProt.ws::select(   up,    column = c(\"keyword\"),    keys = fasta_df$protein_id,    keytype = \"EMBL-GenBank-DDBJ_CDS\"   ) library(dplyr)  keywords_count <- keywords %>%   # Separate the Keywords into different rows   tidyr::separate_rows(Keywords, sep = \";\") %>%   # Replace NA values with 'Other'   mutate(Keywords = replace(Keywords, is.na(Keywords), \"Other\")) %>%   # Add a Count column that counts each Keyword   add_count(Keywords)  # Keep top ranking keywords for each protein ID keywords_count <- keywords_count %>%   group_by(From) %>%   filter(rank(-n, ties.method = \"first\") == 1) %>%   ungroup()  # Replace any keyword that has a count less then 10 with \"Other\" keywords_count <- keywords_count %>%   mutate(Keywords = ifelse(n < 10, \"Other\", Keywords))  # Bind Keywords back to fasta_df fasta_df_with_keywords <-    left_join(fasta_df, keywords_count, by = c(\"protein_id\" = \"From\")) %>%    mutate(Keywords = replace(Keywords, is.na(Keywords), \"Other\")) %>%   select(cluster, start, end, strand, protein_id, protein, Keywords, n) key_legend <- c(setdiff(sort(unique(fasta_df_with_keywords$Keywords)), \"Other\"), \"Other\")  # Make the cluster chart chart <- GC_chart(   fasta_df_with_keywords,   start = \"start\",   end = \"end\",   strand = \"strand\",   group = \"Keywords\",   cluster = \"cluster\",   height = \"400px\" ) %>%    GC_clusterLabel(unique(fasta_df$cluster)) %>%   GC_legend(order = key_legend) %>%   GC_tooltip(     formatter = \"     ProteinID:<\/b> {protein_id}
     Region:<\/b> {start} - {end}     \"   ) chart"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGFF.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Loading Gene Clusters From Generic Feature Format (GFF) Files","text":"tutorial demonstrates creating gene cluster visualizations Generic Feature Format (GFF) files using geneviewer. can obtain .gff files variety platforms NCBI, Ensembl UCSC. tutorial demonstrates load visualize several viral genomes .gff format using geneviewer.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGFF.html","id":"materials","dir":"Articles","previous_headings":"","what":"Materials","title":"Loading Gene Clusters From Generic Feature Format (GFF) Files","text":".gff files retrieved Ensembl website searching respective GenBank identifiers downloading records GFF3 format. Alternatively, files can also directly accessed geneviewer-tutorials repository.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGFF.html","id":"loading-gff-files","dir":"Articles","previous_headings":"","what":"Loading GFF files","title":"Loading Gene Clusters From Generic Feature Format (GFF) Files","text":"can load .gff files R using read_gff function geneviewer package. , can either load file individually specifying file path, load files specifying directory contains .gff files. example , load .gff files specified directory using fields parameter select specific fields loading. fields specified, fields loaded default. Using dplyr package, filter data select entries ‘type’ column contains ‘CDS’. addition add extra column maps GenBank ID filename column corresponding viral name. can now visualize genomic data using geneviewer. chart displays start end positions genes viral genome oriented according strand location. custom title added chart, gene clusters labeled viral names. axis set range facilitate size comparisons among genomes. Additionally, visual representation genes simplified removing outlines (strokes) using smaller markers. final touch change tooltip display gene Name.","code":"library(geneviewer) library(dplyr) # change the path to where you have saved the  # file or the directory containing all .gff files folder_path <- \"~/path/to/folder/\" gff <- read_gff(   folder_path,    fields = c(\"source\", \"type\", \"start\", \"end\", \"strand\", \"Name\")   ) %>%   dplyr::filter(type == \"CDS\")  # Add viral names virus_names <- c(   GU071086 = \"Marseillevirus\",    HQ113105.1 = \"Lausannevirus\",   KF261120 = \"Cannesvirus\",   KF483846 = \"Tunisvirus\" ) gff <- gff %>% mutate(Name = virus_names[filename])   View(gff) # Inspect the data frame in Rstudio GC_chart(gff,           start = \"start\",           end = \"end\",           strand = \"strand\",           cluster = \"Virus\",          height = \"400px\",          ) %>%   GC_title(     \"Marseilleviridae<\/i> viral genomes\",      height = \"40px\") %>%   GC_clusterLabel() %>%   GC_scale(axis_type = \"range\") %>%   GC_genes(     group = \"filename\",      stroke = \"none\",      marker_size = \"small\"     ) %>%   GC_tooltip(formatter = \"Gene:<\/b> {Name}\")"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGenBankFiles.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Loading Gene Clusters From Genbank Files","text":"tutorial demonstrates creating gene cluster visualizations GenBank files using geneviewer. guidance importing clusters FASTA files see: link. can obtain GenBank files containing genomic data variety platforms NCBI, Ensembl, UCSC, antiSMASH MIBiG. geneviewer designed handle GenBank files sources (please report compatibility issues Github), tutorial specifically aims replicate gene cluster visualization found MIBiG website.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGenBankFiles.html","id":"materials","dir":"Articles","previous_headings":"","what":"Materials","title":"Loading Gene Clusters From Genbank Files","text":".gbk files can downloaded MIBiG website following instructions directly geneviewer-tutorials repository.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGenBankFiles.html","id":"loading-genbank-file","dir":"Articles","previous_headings":"","what":"Loading GenBank file","title":"Loading Gene Clusters From Genbank Files","text":"GenBank files MIBiG include additional details, enabling us color-code genes function, use reproduce visualizations show website. Begin downloading GenBank file MIBiG website. tutorial use genbank file gene cluster BGC0000001. Simply click “Download GenBank file” link save file. can load file R using read_gbk function geneviewer. create list containing sections features found GenBank file. can inspect .gbk using View pane Rstudio (use View(gbk)) simply opening .gbk file text editor. visualization interested start end position gene well identifiers functions. can find FEATURES > CDS. Lets print first CDS see information contains. can bind information CDS data.frame using gbk_features_to_df function. code define feature keys interested bind data.frame. set process_region TRUE extract strand, start end region key.","code":"library(geneviewer) # change the path to where you have saved the file file_path <- \"~/path/to/file/BGC0000001.gbk\" gbk <- read_gbk(file_path) View(gbk) # Inspect the list in Rstudio CDS_1 <- gbk[[\"BGC0000001\"]][[\"FEATURES\"]][[\"CDS\"]][[1]]  df <- data.frame(values = CDS_1) df cds_df <- gbk_features_to_df(   gbk,    feature = \"CDS\",   keys = c(\"region\", \"gene\", \"protein_id\", \"gene_kind\", \"product\"),    process_region = TRUE   )"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGenBankFiles.html","id":"cluster-visualization","dir":"Articles","previous_headings":"","what":"Cluster Visualization","title":"Loading Gene Clusters From Genbank Files","text":"can see NA values gene_kind column replace “”. done ready make cluster visualization. make chart similar one find MIBiG website can add title, alter coloring appearance genes add scale. addition, alter tooltip display gene, product region hoover.","code":"# replace NA with \"other\" for gene_kind cds_df$gene_kind[is.na(cds_df$gene_kind)] <- \"other\"  # Make the cluster chart chart <- GC_chart(   cds_df,   start = \"start\",   end = \"end\",   group = \"gene_kind\",   strand = \"strand\",   height = \"130px\" ) chart colors <- list(   \"biosynthetic\" = \"#810E15\",    \"biosynthetic-additional\" = \"#F16D75\",    \"transport\" = \"#6495ED\",   \"regulatory\" = \"#2E8B57\",    \"other\" = \"#808080\" )  chart %>%   GC_genes(     marker = \"boxarrow\",     marker_size = \"small\"   ) %>%   GC_title(     \"BGC0000001: abyssomicin C biosynthetic gene cluster     from Verrucosispora maris<\/i> AB-18-032\",     align = \"left\",     titleFont = list(       fontSize = \"12px\"     )     ) %>%   GC_scale() %>%   GC_color(customColors = colors) %>%   GC_legend(order = names(colors)) %>%   GC_tooltip(     formatter = \"     Gene:<\/b> {gene}
     Product:<\/b> {product}
     Region:<\/b>{start} - {end}     \"   )"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGenBankFiles.html","id":"loading-multiple-genbank-files","dir":"Articles","previous_headings":"","what":"Loading Multiple GenBank files","title":"Loading Gene Clusters From Genbank Files","text":"functions read transfom .gbk files can also used load multiple .gbk files folder shown clusters side side. demonstrate can go cluster page BGC0000001 navigate “KnownClusterBlast” page. Click homologous clusters download .gbk files BGC0001694, BGC0001492, BGC0001288 BGC0000133. place .gbk files directory can load together done previously. now list .gbk files containing different sections features. can use gbk_features_to_df function make data.frame features. time besides CDS also make data.frame source can add Organism name genomic region title cluster. can now plot graph time specify “cluster” column identifier distinguish clusters add cluster labels titles.","code":"library(geneviewer) # change the path to the folder containing the .gbk files folder_path <- \"~/path/to/folder/\" gbk <- read_gbk(folder_path) View(gbk) # Inspect the list in Rstudio cds_clusters_df <- gbk_features_to_df(   gbk_list,    feature = \"CDS\",   keys = c(\"region\", \"gene\", \"protein_id\", \"gene_kind\", \"product\"),    process_region = TRUE   ) source_clusters_df <- gbk_features_to_df(gbk_list, feature = \"source\") #> Warning in gbk_features_to_df(gbk_list, feature = \"source\"): Feature source not #> found in cluster BGC0001004 #> Warning in gbk_features_to_df(gbk_list, feature = \"source\"): Feature source not #> found in cluster BGC0001204 #> Warning in gbk_features_to_df(gbk_list, feature = \"source\"): Feature source not #> found in cluster BGC0002124 # replace NA with \"other\" for gene_kind cds_clusters_df$gene_kind[is.na(cds_clusters_df$gene_kind)] <- \"other\"  colors <- list(   \"biosynthetic\" = \"#810E15\",    \"biosynthetic-additional\" = \"#F16D75\",    \"transport\" = \"#6495ED\",   \"regulatory\" = \"#2E8B57\",    \"other\" = \"#808080\" )  # Make the cluster chart GC_chart(   cds_clusters_df,   start = \"start\",   end = \"end\",   group = \"gene_kind\",   strand = \"strand\",   cluster = \"cluster\",   height = \"800px\" ) %>%     GC_clusterTitle(     y = 5,       title = paste0(\"\", source_clusters_df$organism, \"<\/i>: \", source_clusters_df$region),     align = \"left\",     titleFont = list(fontSize = 12),     ) %>%   GC_clusterLabel(names(gbk_list)) %>%   GC_genes(     marker = \"boxarrow\",     marker_size = \"small\"   ) %>%   GC_scaleBar(title = \"1kb\", scaleBarUnit = 1000) %>%   GC_color(customColors = colors) %>%   GC_legend(order = names(colors)) %>%   GC_tooltip(     formatter = \"     Gene:<\/b> {gene}
     ProteinID:<\/b> {protein_id}
     Product:<\/b> {product}
     Region:<\/b>{start} - {end}     \"   )"},{"path":"https://nvelden.github.io/geneviewer/articles/MUMMER.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Genome alignment using MUMmer","text":"tutorial guides process performing genome alignments using MUMmer, alignment tool widely used comparing genomic sequences. example align plasmids serveral species B. thuringiensis. Following alignment, ’ll show visualize results using geneviewer.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/MUMMER.html","id":"materials","dir":"Articles","previous_headings":"","what":"Materials","title":"Genome alignment using MUMmer","text":".gbk files can downloaded directly GenBank using accession numbers CP000486.1, CP009599.1, CP003188.1 CP009638.1. Alternatively, can obtain GenBank files including alignment files directly geneviewer-tutorials repository.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/MUMMER.html","id":"mummer-alignment","dir":"Articles","previous_headings":"","what":"MUMmer alignment","title":"Genome alignment using MUMmer","text":"MUMmer needs installed local machine execute alignments. detailed installation instructions, visit MUMmer website. MUMmer installed, can perform alignment using geneviewer mummer_alignment() function. default run alignment order files folder. Important MUMmer requires file paths without spaces. default, mummer_alignment() function perform pair wise alignments starting first file folder. adjust order files aligned, assign vector file names cluster variable. default nucleotide sequences translated proteins using “promer” “many--many” mapping alignment performed. suitable alignment method project, please carefully review MUMmer documentation. learn modify default settings, consult documentation running ?mummer_alignment(). alignment generates data frame details start end positions aligned region reference (cluster1) query (cluster2), along identity similarity scores. data frame can directly loaded GC_links() function.","code":"library(geneviewer) # Change the path to the folder where the .gbk files are saved folder_path <- \"~/path/to/folder/\" alignment <-    mummer_alignment(     path = folder_path,     cluster = NULL,     maptype = \"many-to-many\",     seqtype = \"protein\"   )"},{"path":"https://nvelden.github.io/geneviewer/articles/MUMMER.html","id":"synteny-gene-cluster-chart","dir":"Articles","previous_headings":"","what":"Synteny gene cluster chart","title":"Genome alignment using MUMmer","text":"map alignment onto genome, must first load cluster information .gbk files. detailed instructions, please refer tutorial Load Gene Cluster data GenBank Files. add extra column called “CDS” data used key color genes. can load cluster data GC_chart() alignment data GC_links() function. addition, change axis_type “range”, make genes little smaller add cluster labels. customization options see Get started. Important: gene cluster data like alignment data loaded order files folder. custom order used MUMer alignment make sure sort “cluster” column cluster data way.","code":"folder_path <- \"~/path/to/folder/\" gbk <- read_gbk(folder_path) cds_df <- gbk_features_to_df(   gbk,    feature = \"CDS\",   keys = c(\"region\", \"gene\", \"protein_id\", \"note\", \"product\")   ) cds_df$type <- \"CDS\" GC_chart(   data = cds_df,   group = \"cluster\",   strand = \"strand\",   cluster = \"cluster\" ) %>% GC_links(   data = alignment,   measure = \"identity\", # similarity/none ) %>% GC_scale(axis_type = \"range\") %>% GC_cluster(separate_strands = TRUE) %>% GC_genes(   group = \"type\",   marker_size = \"small\" ) %>%     GC_clusterLabel(   title = c(\"pALH1\", \"pBFQ\", \"F837_55\", \"pBFI_4\"),    width = 50   ) %>% GC_tooltip(   formatter = \"{protein_id}<\/b>
{start} - {end}\"  ) %>% GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/Transcripts.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Visualizing gene Transcripts","text":"tutorial shows use biomaRt load transcript data Ensembl visualize using geneviewer. practical example, retrieve exon UTR regions five different splice variants BRCA1 gene display results geneviewer.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/Transcripts.html","id":"loading-transcript-data","dir":"Articles","previous_headings":"","what":"Loading Transcript data","title":"Visualizing gene Transcripts","text":"Transcript data BRCA1 gene can loaded using biomaRt package, Ensembl gene ID obtained Ensembl website. example, first load necessary libraries. Next, specify Ensembl gene ID BRCA1 establish connection Ensembl database using useMart(). Finally, retrieve transcript IDs associated BRCA1 gene using getBM() function. Now transcript IDs associated BRCA1 gene, can retrieve start end positions exons, well 5’ 3’ UTRs. Additionally, add strand information transcript. example, retrieve information first 5 transcript IDs. use getBM function retrieve start end positions feature separately. rename start end columns, allowing us combine results single data frame using bind_rows dplyr package. Finally, remove rows NA start column add strand information transcript. Now start, end strand information transcripts can visualize results using geneviewer GC_transcript function. Note intron positions calculated based exon positions. ensure exons recognized, type column feature name must specified include “exon” name. can customize chart adding title transcript name footer relative abundance transcript. change color, alter appearance specific features, explore many options, see Get Started guide GC_transcripts documentation running ?GC_transcripts console.","code":"library(biomaRt) library(geneviewer) library(dplyr)   ensembl_gene_id <- c(\"ENSG00000012048\") mart = useMart(\"ensembl\", dataset = \"hsapiens_gene_ensembl\")  # Retrieve all transcript IDs for the gene transcrips <- getBM(attributes = c(\"ensembl_gene_id\", \"ensembl_transcript_id\"),                               filters = \"ensembl_gene_id\",                               values = ensembl_gene_id,                               mart = mart) transcript_IDs <- transcrips$ensembl_transcript_id[1:5]  # Get exon details exon_attributes <- c(\"ensembl_transcript_id\", \"exon_chrom_start\", \"exon_chrom_end\") exon_results <- getBM(attributes = exon_attributes,                       filters = \"ensembl_transcript_id\",                       values = transcript_IDs,                       mart = mart) %>%   dplyr::mutate(type = \"exon\", start = exon_chrom_start, end = exon_chrom_end) %>%   dplyr::select(ensembl_transcript_id, type, start, end)  # Get 3' UTR details utr3_attributes <- c(\"ensembl_transcript_id\", \"3_utr_start\", \"3_utr_end\") utr3_results <- getBM(attributes = utr3_attributes,                       filters = \"ensembl_transcript_id\",                       values = transcript_IDs,                       mart = mart) %>%   dplyr::mutate(type = \"3_utr\", start = `3_utr_start`, end = `3_utr_end`) %>%   dplyr::select(ensembl_transcript_id, type, start, end)  # Get 5' UTR details utr5_attributes <- c(\"ensembl_transcript_id\", \"5_utr_start\", \"5_utr_end\") utr5_results <- getBM(attributes = utr5_attributes,                       filters = \"ensembl_transcript_id\",                       values = transcript_IDs,                       mart = mart) %>%   dplyr::mutate(type = \"5_utr\", start = `5_utr_start`, end = `5_utr_end`) %>%   dplyr::select(ensembl_transcript_id, type, start, end)  # Bind features transcript_attributes <- bind_rows(exon_results, utr3_results, utr5_results) %>%   filter(!is.na(start))  # Add strand transcript_strand <- getBM(attributes = c(\"ensembl_transcript_id\", \"strand\"),                            filters = \"ensembl_transcript_id\",                            values = transcript_IDs,                            mart = mart)   # Add transcript strand transcript_attributes <-    dplyr::left_join(     transcript_attributes,      transcript_strand,      by = \"ensembl_transcript_id\"     ) GC_chart(   data = transcript_attributes,    start = \"start\",   end = \"end\",   strand = \"strand\",   height = \"600px\" ) %>%   GC_transcript(     transcript = \"ensembl_transcript_id\",     type = \"type\"   ) GC_chart(   data = transcript_attributes,    height = \"600px\"   ) %>%   GC_transcript(     transcript = \"ensembl_transcript_id\",      strand = \"strand\",      type = \"type\",   ) %>%   GC_clusterTitle(     title = unique(transcript_attributes$ensembl_transcript_id),     titleFont = list(       fontSize = \"12px\"     )   ) %>%   GC_clusterFooter(     title = c(\"0.8%\", \"0.1%\", \"0.07%\", \"0.02%\", \"0.01%\"),     align = \"center\"   )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"geneviewer","text":"geneviewer available GitHub","code":"# install.packages(\"devtools\") devtools::install_github(\"nvelden/geneviewer\")"},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"single-gene-cluster","dir":"Articles","previous_headings":"Cluster Visualization","what":"Single Gene Cluster","title":"geneviewer","text":"visualize single gene cluster, minimum requirements start end positions gene, typically named “start” “end”. addition group can defined used color coding genes used default categorical variable legend.","code":"# Example data for a single Gene cluster ophA_cluster <- subset(ophA_clusters, cluster == \"ophA\")  GC_chart(ophA_cluster,           start = \"start\",           end = \"end\",           group = \"class\",           height = \"150px\"          )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"multiple-gene-clusters","dir":"Articles","previous_headings":"Cluster Visualization","what":"Multiple Gene Clusters","title":"geneviewer","text":"visualizing multiple gene clusters, additional variable needed used define clusters (shown ‘cluster’ column ). example overall chart height set “300px”. Since two distinct gene clusters height cluster 150px.","code":"# Example data for two Gene clusters GC_chart(ophA_clusters,           start = \"start\",           end = \"end\",           group = \"class\",           cluster = \"cluster\",           height = \"300px\"          )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"styling","dir":"Articles","previous_headings":"Cluster Visualization","what":"Styling","title":"geneviewer","text":"customize overall appearance chart, can use style parameter, accepts list CSS style properties. styling specific elements individually, please refer corresponding functions listed .","code":"# Example data for two Gene clusters GC_chart(ophA_clusters,           start = \"start\",           end = \"end\",           group = \"class\",           cluster = \"cluster\",           height = \"200px\",          style = list(            border = \"1px solid black\",            backgroundColor = \"#FAEBD7\"            # Any other CSS style            )          )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"shiny","dir":"Articles","previous_headings":"","what":"Shiny","title":"geneviewer","text":"GC_chartOutput() renderGC_chart() functions enable visualize gene clusters within Shiny applications.","code":"# Load necessary libraries library(shiny) library(geneviewer)   # Define UI ui <- fluidPage(titlePanel(\"Omphalotin Gene Cluster Visualization\"),                 mainPanel(# Output for GC_chart                   GC_chartOutput(                     \"gcChart\", width = \"100%\", height = \"400px\"                   )))  # Define server logic server <- function(input, output) {   output$gcChart <- renderGC_chart({          GC_chart(       ophA_clusters,       cluster = \"cluster\",       group = \"class\"     ) %>%       GC_clusterTitle(title = c(\"O. olearius<\/i>\", \"D. bispora<\/i>\")) %>%       GC_labels(\"name\") %>%       GC_legend(position = \"bottom\") %>%       GC_scaleBar() %>%       GC_clusterLabel(title = \"ophA\")        }) }  # Run the application shinyApp(ui = ui, server = server)"},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"specific-clusters","dir":"Articles","previous_headings":"Selections","what":"Specific Clusters","title":"geneviewer","text":"Customization functions default set alter styling gene clusters across chart. select specific cluster one can use cluster variable available customization functions. can select cluster either ’s name number. example y position adjusted first cluster shifting labels cluster.","code":"GC_chart(ophA_clusters, cluster = \"cluster\", group = \"class\", height = \"350px\") %>%   GC_title(title = \"ophA Gene Clusters\") %>%   GC_labels(label = \"name\", cluster = \"ophA\", y = 18) %>%   GC_labels(label = \"name\", cluster = 2)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"individual-items","dir":"Articles","previous_headings":"Selections","what":"Individual Items","title":"geneviewer","text":"apply styling particular item within gene cluster, itemStyle variable can used. variable, accessible customization functions, requires list specifies index number desired item along intended styling attributes. ’s important note indexing itemStyle begins 0, following zero-based numbering system. example , 3rd label ophA cluster styled red color bold font. code also customizes labels cluster 2, 5th label similarly styled red bold, 4th label’s position adjusted.","code":"GC_chart(ophA_clusters, cluster = \"cluster\", group = \"class\", height = \"300px\") %>%   GC_title(title = \"ophA Gene Clusters\", height = \"30px\") %>%   GC_labels(label = \"name\",              cluster = \"ophA\",              itemStyle =                list(                 list(index = 2, fill = \"red\", fontWeight = \"bold\")                 )             ) %>%   GC_labels(     label = \"name\",      cluster = 2,     itemStyle =                list(                 list(index = 4, fill = \"red\", fontWeight = \"bold\"),                 list(index = 3, y = 10, x = -5)                 )     )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"cluster","dir":"Articles","previous_headings":"","what":"Cluster","title":"geneviewer","text":"GC_cluster function can used style adjust margins specific clusters. example set different background color cluster decrease left right margins 25px. Note margins title legend adjusted. adjust well easiest use GC_grid function adjust margins elements .","code":"GC_chart(   ophA_clusters,   group = \"class\",   cluster = \"cluster\",   height = \"300px\"    ) %>%   GC_title(\"Adjust margins of GC clusters\", align = \"left\", height = \"40px\") %>%   GC_cluster(margin = list(left = 25, right = 25)) %>%   GC_cluster(cluster = 1, style = list(backgroundColor = \"green\")) %>%   GC_cluster(cluster = 2, style = list(backgroundColor = \"red\"))"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"separation-of-forward-and-reverse-strands","dir":"Articles","previous_headings":"Cluster","what":"Separation of Forward and Reverse strands","title":"geneviewer","text":"Forward reverse strands can separated distinct tracks. example forward reverse strands separated second cluster. vertical spacing slightly increased (default = 0). Note: GC_cluster() function must called setting genes, labels coordinates proper effect.","code":"GC_chart(   ophA_clusters,   group = \"name\",   cluster = \"cluster\",   height = \"350px\"    ) %>%    GC_labels() %>%   GC_cluster(separate_strands = TRUE, strand_spacing = 3) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"prevent-gene-overlap","dir":"Articles","previous_headings":"Cluster","what":"Prevent Gene Overlap","title":"geneviewer","text":"prevent gene overlaps, genes automatically separated distinct tracks. GC_cluster function track-based separation can switched spacing tracks can adjusted. example track switched first cluster spacing second cluster increased 40 50. Note: Setting separate_strands prevent_gene_overlap TRUE supported moment.","code":"GC_chart(   subset(human_hox_genes, cluster %in% c(\"HOXA\", \"HOXB\")),   group = \"name\",   cluster = \"cluster\",   height = \"300px\"    ) %>%    GC_labels(label = \"name\", adjustLabels = FALSE) %>%   GC_labels(label = \"name\",              cluster = 2,              itemStyle = list(list(index = 5, x=10))             ) %>%   GC_cluster(prevent_gene_overlap = TRUE, overlap_spacing = 30) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"grid","dir":"Articles","previous_headings":"","what":"Grid","title":"geneviewer","text":"GC_grid() function can used modify grid chart specific clusters. example top bottom margins increased left right margins decreased 50px default 25px. Clusters can shown side side setting direction row adjusting width cluster.","code":"GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\",          style = list(backgroundColor = \"red\"),          height = \"300px\"          ) %>%   GC_title(     \"Adjusting Margins of a GC_chart\",      align = \"left\",      y = 15,      style = list(backgroundColor = \"yellow\",                   align = \"left\")     ) %>%   GC_cluster(style = list(backgroundColor = \"green\")) %>%   GC_legend(TRUE, style = list(backgroundColor = \"yellow\")) %>%   GC_grid(margin = list(top = 50, bottom = 50, left = 25, right = 25)) GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"250px\") %>%   GC_grid(direction = \"row\", margin = list(left = 15, right = 15)) %>%   GC_clusterTitle(c(\"Omphalotus Olearius<\/i>\", \"Dendrothele Bisporus<\/i>\")) %>%   GC_legend(position = \"top\") %>%   GC_grid(     cluster = c(1,2),      width = \"50%\",     height = \"50%\"   )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"genes","dir":"Articles","previous_headings":"","what":"Genes","title":"geneviewer","text":"GC_genes() function can used custom style genes. example stroke stroke width altered can take valid CSS style. color coding set according group GC_chart() function. Changing color scheme best done GC_color() function (see: Colors section) uniformly change colors genes legend. default genes displayed arrows. alter appearance one can use marker marker_size variables. Beside default arrow marker one can use boxarrow, box, rbox cbox. can set marker small, medium (default) large. finer control one can use markerHeight variable overwrite marker_size variable. addition can change position markers using x y variables. case arrow boxarrow markers can also alter arrowhead using arrowheadWidth arrowheadHeight variables.","code":"GC_chart(ophA_cluster, cluster = \"cluster\", group = \"class\", height = \"150px\") %>%   GC_genes(     show = TRUE,     stroke = \"grey\",     strokeWidth = 2     # Any other CSS style   ) %>%    GC_color(colorScheme = \"schemeAccent\") %>%    GC_legend() GC_chart(ophA_cluster, cluster = \"cluster\", group = \"class\", height = \"100px\") %>%   GC_genes(marker = \"arrow\", marker_size = \"small\") %>%   GC_clusterLabel(\"arrow\") %>%    GC_legend(FALSE) GC_chart(ophA_cluster, cluster = \"cluster\", group = \"class\", height = \"100px\") %>%   GC_genes(     y = 55,     marker = \"arrow\",      markerHeight = 10,     arrowheadHeight = 15,     arrowheadWidth = 15     ) %>%   GC_clusterLabel(\"customized arrows\") %>%    GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"gene-alignment","dir":"Articles","previous_headings":"","what":"Gene alignment","title":"geneviewer","text":"GC_align() function can used align specific gene across clusters. example , specify column contains gene identifiers vertically align gene across clusters left. Please note gene identifier used alignment must across clusters unique within cluster.","code":"GC_chart(ophA_clusters, cluster = \"cluster\", group = \"class\", height = \"150px\") %>%    GC_align(      id_column = \"class\",       id = \"NTF2-like\",      align = \"left\" # center / right      ) %>%    GC_legend(TRUE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"gene-normalization","dir":"Articles","previous_headings":"","what":"Gene normalization","title":"geneviewer","text":"GC_normalize function can used normalize genomic coordinates set genes within cluster, ensuring genes evenly spaced along entire range cluster. example normalize genes first cluster even spacing genes preserving original length. Optionally, custom spacing genes can set using gap variable. Note: Normalization adjust start end positions genes, causing differ original coordinates. display original start end positions tooltip, formatter can updated use original_start original_end values. can adjust spacing specific genes using custom_gaps variable. example , normalize spacing genes first cluster, set uniform gap width genes, increase gap 1.5x genes ophC ophB2.","code":"GC_chart(ophA_clusters, cluster = \"cluster\", group = \"class\", height = \"150px\") %>%    GC_normalize(      group = \"class\",       cluster = 1, # By default all clusters are normalized      gap = NULL, # 0-1      preserve_gene_length = TRUE      ) %>%   # Update tooltip   GC_tooltip(     cluster = 1,     formatter = \"Start:<\/b> {original_start}
End:<\/b> {original_end}\"   ) %>%   GC_legend(FALSE) GC_chart(ophA_clusters, cluster = \"cluster\", group = \"class\", height = \"280px\") %>%    GC_normalize(      group = \"name\",       cluster = 1, # By default all clusters are normalized      gap = 0.01, # 0-1      custom_gaps = list(ophC = 1.5, ophB2 = 1.5),      preserve_gene_length = FALSE      ) %>%   GC_labels(label = \"name\") %>%   # Update tooltip   GC_tooltip(     cluster = 1,     formatter = \"Start:<\/b> {original_start}
End:<\/b> {original_end}\"   ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"blastp","dir":"Articles","previous_headings":"","what":"BlastP","title":"geneviewer","text":"protein_blast() function can used perform BlastP alignment clusters. information see Cluster comparison using BlastP tutorial.","code":"BlastP_results <-    protein_blast(     data, # or path to folder containing .gbk files     query, # The name of the query cluster to be used for BLAST comparisons.     id = \"protein_id\", # The name of the column that contains the gene identifiers.     start = \"start\",     end = \"end\",     cluster = \"cluster\",     genes = NULL, #Vector of protein IDs to include for BlastP analysis.     identity = 30,     parallel = TRUE )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"transcripts","dir":"Articles","previous_headings":"","what":"Transcripts","title":"geneviewer","text":"GC_transcript() function can used visualize transcripts. requires setting transcript column unique IDs transcript type column identifying whether feature “UTR”, “exon”. Optionally, can also set direction specifying strand column. Please note introns calculated based exon positions. wide range options customize exons, introns UTRs. options see documentation running ?GC_transcript(). Junctions can added transcripts using Arc annotation. example setting custom colors grouping “type” specifying colors using customColors. introns, exons, UTRs, labels can styled using styleIntrons, styleExons, styleUTRs, labelOptions variables respectively. itemStyle combination selection variable allows customization individual exons, introns, UTRs within specific transcripts.","code":"transcript_data <- data.frame(   transcript = c(\"transcript1\", \"transcript1\", \"transcript1\", \"transcript1\",                  \"transcript2\", \"transcript2\", \"transcript2\"),   type = c(\"5_utr\", \"exon\", \"exon\", \"3_utr\",            \"5_utr\", \"exon\", \"3_utr\"),   start = c(1, 101, 201, 301,             1, 101, 301),   end = c(50, 150, 250, 350,           50, 150, 350),   strand = rep(\"forward\", 7) )  GC_chart(   transcript_data,    start = \"start\",   end = \"end\",   height = \"200px\") %>% GC_transcript(   transcript = \"transcript\",    strand = \"strand\",  ) GC_chart(   transcript_data,    start = \"start\",   end = \"end\",   height = \"200px\"   ) %>%   GC_transcript(     group = \"type\",     customColors =        list(         exon = \"green\",         intron = \"blue\",         `5_utr` = \"black\",         `3_utr` = \"grey\"       )     ) GC_chart(transcript_data, height = \"200px\") %>%   GC_transcript(     styleIntrons =        list(       strokeWidth = 2,       markerHeight = 60       # Any other CSS style       ),     styleExons =        list(         markerSize = \"small\",         fill = \"none\",         strokeWidth = 2,         stroke = \"red\"         # Any other CSS style       ),     styleUTRs = list(       marker = \"boxarrow\",       markerSize = \"small\",       fill = \"green\"       # Any other CSS style     ),     labelOptions = list(       show = TRUE,       xOffset = 0,       yOffset = 0,       fontSize = \"10px\",       fontWeight = \"bold\"       # Any other CSS style     )   ) GC_chart(   transcript_data,    start = \"start\",   end = \"end\",   height = \"200px\"   ) %>%   GC_transcript(     transcript = \"transcript\",     selection = 1,     itemStyleExons =        list(         list(index = 0, fill = \"red\")       )   ) %>%   GC_transcript(     transcript = \"transcript\",     selection = 2,     itemStyleIntrons =      list(       list(index = 1, stroke = \"red\", strokeWidth = 2)     )   )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"links","dir":"Articles","previous_headings":"","what":"Links","title":"geneviewer","text":"get_links GC_links() functions can used add links genes. example, initially create chart object. Subsequently, generate links among clusters. achieved specifying grouping column generate links value pairs different clusters. Using value1 value2 variables get_links function can generate links specific genes. case 2 clusters can use cluster variable allows specify clusters generate links . “identity” “similarity” column can added data used measure set color intensity links. addition links labels can styled using linkStyle labelStyle variable. data parameter allows load data frame defines links genomic regions start end positions, rather linking specific genes. can include “identity” “similarity” column used set color intensity links.","code":"# Generate chart object chart <- GC_chart(   ophA_clusters,    cluster = \"cluster\",    group = \"class\",    height = \"250px\") %>%   GC_legend(FALSE)  # Add links to chart chart %>% GC_links(\"class\") # Add links to chart chart %>%    GC_links(     \"name\",      value1 = c(\"ophB1\", \"ophC\"),      value2 = c(\"dbophB1\", \"dbophC\"),     cluster = c(1,2)     ) %>%    GC_labels(\"name\") ophA_clusters$identity <- sample(1:100, size = nrow(ophA_clusters), replace = TRUE)  ophA_clusters$identity[ophA_clusters$cluster == \"ophA\"] <- NA  chart <- GC_chart(   ophA_clusters,    cluster = \"cluster\",    group = \"class\",    height = \"250px\") %>%   GC_links(     \"class\",      value1 = c(\"Methyltransferase\", \"Prolyloligopeptidase\"),      value2 = c(\"Methyltransferase\", \"Prolyloligopeptidase\"),     inverted_color = \"green\",      measure = \"identity\", # similarity / none     label = TRUE,     curve = FALSE,     color_bar = TRUE,     colorBarOptions = list(        x = 0,        y = 24,        width = 10,        height = 60,        labelOptions = list(          fontSize = 8,          xOffset = 2,          yOffset = 0          # Any other CSS style        ),        titleOptions = list(          fontSize = 10,          xOffset = 2,          yOffset = 0          # Any other CSS style        ),        barOptions = list(          stroke = \"#000\",          strokeWidth = 0.5,          opacity = 1          # Any other CSS style        )      ),     linkStyle = list(       stroke = \"black\",       strokeWidth = 0.5       # Any other CSS style     ),     labelStyle = list(       fill = \"red\"       # Any other CSS style     )     ) %>%    GC_legend(TRUE)  chart links_data <- data.frame(   start1 = c(5000, 16000),   end1 =  c(9000, 19000),   start2 = c(20000, 42000),   end2 = c(25000, 32000),   cluster1 = c(\"ophA\",\"ophA\"),   cluster2 = c(\"dbophA\", \"dbophA\"),   identity = c(20, 100),   similarity = c(10, 90) ) # Add links to chart GC_chart(   ophA_clusters,    cluster = \"cluster\",    group = \"class\",    height = \"250px\") %>%    GC_links(     data = links_data,     measure = \"identity\"     )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"sequence","dir":"Articles","previous_headings":"","what":"Sequence","title":"geneviewer","text":"sequence line GC_sequence() function initially presented solid black line, can customized sequenceStyle option. Additionally, markerStyle option allows adjusting style break markers.","code":"GC_chart(   ophA_clusters, group = \"class\",   cluster = \"cluster\",   height = \"150px\") %>%   GC_sequence(     show = TRUE,     cluster = NULL,     y = 50,     sequenceStyle = list(       stroke = \"grey\",       strokeWidth = 1       # Any other CSS style     ),     markerStyle = list(       stroke = \"grey\",       strokeWidth = 1,       gap = 3,       tiltAmount = 5       # Any other CSS style     )   ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"labels","dir":"Articles","previous_headings":"","what":"Labels","title":"geneviewer","text":"gene cluster one can add title, gene labels, cluster label footer shown example . adjust positioning labels, x, y, align variables can used. Note example, GC_labels() employed twice: initially, sets labels uniformly gene clusters, specifically adjusts fourth eight label (considering index starts 0) cluster 2, ensure overlap. adjust position styling specific labels one can use cluster itemStyle variables. cluster variable one can select specific cluster name number. Using itemStyle variable one can provide list index number specific label styles applied . Note index itemStyle starts 0.","code":"GC_chart(ophA_clusters,           start = \"start\",           end = \"end\",           group = \"class\",           cluster = \"cluster\",           height = \"450px\"          ) %>%   GC_clusterTitle(     title = c(\"Omphalotus Olearius<\/i>\", \"Dendrothele Bisporus<\/i>\"),      titleFont = list(fontWeight = \"normal\")     ) %>%   GC_labels(\"name\") %>%   GC_clusterLabel(title = unique(ophA_clusters$cluster)) %>%   GC_clusterFooter(     x = 100,     title = c(\"Nr. of Genes: 7\", \"Nr. of Genes: 10\"),      subtitle = c(\"Locus: 2522 - 21,484\", \"Locus 19,236 - 43,005\")     ) %>%   GC_legend(position=\"top\") GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"360px\") %>%   GC_clusterTitle(     c(\"Omphalotus Olearius<\/i>\", \"Dendrothele Bisporus<\/i>\"),      position = \"left\",      x = 20) %>%   GC_labels(\"name\", y = 20) %>%   GC_labels(\"name\",              cluster = 2,              y = 20,              itemStyle =                list(                 list(index = 3, y = 52),                 list(index = 7, y = 52)                 )             ) %>%   GC_clusterFooter(     title = c(\"Nr. of Genes: 7\", \"Nr. of Genes: 10\"),      subtitle = c(\"Locus: 2522 - 21,484\", \"Locus 19,236 - 43,005\"),      align = \"center\"     ) GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"360px\") %>%   GC_labels(\"name\", y = 20) %>%   GC_labels(\"name\",              cluster = 2,              y = 20,             itemStyle = list(               list(index = 3, y = 52, fill = \"red\"),               list(index = 7, y = 52, fill = \"red\")               )             )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"annotations","dir":"Articles","previous_headings":"","what":"Annotations","title":"geneviewer","text":"GC_annotation function can used add annotations specified clusters within GC chart. types annotations available : text, textMarker, line, arrow, symbol, rectangle, promoter, terminator. Annotations placed specifying type followed type specific parameters. shown example multiple annotations type can placed providing list values. GC_trackMouse() function can used track mouse coordinates hoovering chart makes easy determine x y positions place annotation.","code":"GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"300px\") %>%   GC_annotation(     cluster = 1,     type = \"text\",     text = \"Gene 1\",     x = 2970,     y = 60   ) %>%    GC_annotation(     cluster = 2,     type = \"text\",     text = c(\"Gene 1\", \"Gene 2\", \"Gene 3\"),     x = c(19400, 22200, 25600),     y = 60   ) %>%   GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"text","dir":"Articles","previous_headings":"Annotations","what":"Text","title":"geneviewer","text":"shows example options place text annotation. text, x y variables can also take list values.","code":"GC_chart(ophA_cluster, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_annotation(     cluster = 1,     type = \"text\",      text = \"Gene 1\",     x = 2970,     y = 58,     style = list(       fontSize = \"10px\",       fontStyle = \"normal\",       fontWeight = \"normal\",       textDecoration = \"none\",       fontFamily = \"sans-serif\",       cursor = \"default\"       # Any other CSS style     )    ) %>%   GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"text-marker","dir":"Articles","previous_headings":"Annotations","what":"Text Marker","title":"geneviewer","text":"shows example options place text Marker. exception styles variables can also take list values. default x1 x2 NULL position used horizontal placement.","code":"GC_chart(ophA_cluster, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_annotation(     cluster = 1,     type = \"textMarker\",      text = \"Gene 1\",     x1 = NULL,     y1 = 66,     x2 = NULL,     y2 = 50,     position = 9300,     labelX = 0,     labelY = 0,     showArrow = FALSE,     arrowSize = 8,     textStyle = list(       fontSize = \"10px\",       fontFamily = \"sans-serif\",       fill = \"black\",       textAnchor = \"middle\"     ),     arrowStyle = list(       fill = \"black\"     ),     lineStyle = list(       stroke = \"black\",       strokeWidth = 1     )   ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"promoter-terminator","dir":"Articles","previous_headings":"Annotations","what":"Promoter / Terminator","title":"geneviewer","text":"shows example options place promoter. exception styles variables can also take list values.","code":"GC_chart(ophA_cluster, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_annotation(     cluster = 1,     type = \"promoter\", # terminator     x = 9300,     y = 50,      direction = \"forward\", # reverse     style = list(       fill = \"none\",       stroke = \"black\",       strokeWidth = 1       # Any other CSS style     ),     rotation = 0,     scale = 1   ) %>%    GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"symbol","dir":"Articles","previous_headings":"Annotations","what":"Symbol","title":"geneviewer","text":"shows example options place symbol. Supported symbols circle, cross, diamond, square, star, triangle, wye. exception styles variables can also take list values.","code":"GC_chart(ophA_cluster, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_annotation(     cluster = 1,     type = \"symbol\", # circle/cross/diamond/square/star/triangle/wye     symbol = \"circle\",      x = 9300,     y = 50,      size = 64,     rotation = 0,     style = list(       fill = \"black\",       stroke = \"black\",       strokeWidth = 2       # Any other CSS style       )     ) %>%    GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"arrow","dir":"Articles","previous_headings":"Annotations","what":"Arrow","title":"geneviewer","text":"shows example options place arrow. exception styles variables can also take list values.","code":"GC_chart(ophA_cluster, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_annotation(     cluster = 1,     type = \"arrow\",     x1 = 9300,     y1 = 70,     x2 = 9300,     y2 = 50,     arrowSize = 8,     arrowStyle = list(       fill = \"black\"       # Any other CSS style     ),     lineStyle = list(       stroke = \"black\",       strokeWidth = 1       # Any other CSS style     )    ) %>%    GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"line","dir":"Articles","previous_headings":"Annotations","what":"Line","title":"geneviewer","text":"shows example options place line. exception styles variables can also take list values.","code":"GC_chart(ophA_cluster, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_annotation(     cluster = 1,     type = \"line\",     x1 = 9300,     y1 = 70,     x2 = 9300,     y2 = 50,     style = list(       stroke = \"black\",       strokeWidth = 1       # Any other CSS styles     )   ) %>%    GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"arc","dir":"Articles","previous_headings":"Annotations","what":"Arc","title":"geneviewer","text":"shows example options place arcs.","code":"transcript_data <- data.frame(   transcript = c(\"transcript1\", \"transcript1\", \"transcript1\", \"transcript1\"),   type = c(\"5_utr\", \"exon\", \"exon\", \"3_utr\"),   start = c(1, 101, 201, 301),   end = c(50, 150, 250, 350),   strand = rep(\"forward\", 4) )  GC_chart(   transcript_data,    start = \"start\",   end = \"end\",   height = \"200px\") %>% GC_transcript(   transcript = \"transcript\",    strand = \"strand\",  ) %>%   GC_annotation(     cluster = NULL,     type = \"arc\",     x1 = c(150, 50),                        y1 = c(50),                       x2 = c(301, 201),                      y2 = c(50),                       midY = c(80, 20),                     stroke = c(\"black\"),              strokeWidth = c(0.8, 0.1),              labelX = c(0),                    labelY = c(0),                    text = c(0.8, 0.1),                    lineStyle = list(       # Any other CSS styles     ),     textStyle = list(       fontSize = \"10px\",                fontFamily = \"sans-serif\",        fill = \"black\",                  textAnchor = \"middle\"             # Any other CSS styles     )   ) %>%    GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"square","dir":"Articles","previous_headings":"Annotations","what":"Square","title":"geneviewer","text":"shows example options place square. rotation variable can also take list values.","code":"GC_chart(ophA_cluster, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_annotation(     cluster = 1,     type = \"rectangle\",     rotation = 0,     position =        list(         list(c(9200, 60), c(11100, 40)),         list(c(11700, 60), c(12900, 40))         ),     style = list(       stroke = \"black\",       strokeWidth = 1       # Any other CSS styles     )   ) %>%    GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"colors","dir":"Articles","previous_headings":"","what":"Colors","title":"geneviewer","text":"color legend genes can controlled GC_color function using colorScheme customColors variables.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"colorscheme","dir":"Articles","previous_headings":"Colors","what":"colorScheme","title":"geneviewer","text":"Defines predefined color scheme legend, “schemeCategory10” “schemeAccent” D3.js. Supported schemes include: schemeCategory10: array ten categorical colors. schemeAccent: array eight categorical colors. schemeDark2: array eight categorical colors. schemePaired: array twelve categorical colors. schemePastel1: array nine categorical colors. schemePastel2: array eight categorical colors. schemeSet1: array nine categorical colors. schemeSet2: array eight categorical colors. schemeSet3: array twelve categorical colors. schemeTableau10: array ten categorical colors, originally created Tableau.","code":"GC_chart(ophA_cluster, group = \"class\", height = \"100px\") %>%   GC_color(colorScheme = \"schemeAccent\")"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"customcolors","dir":"Articles","previous_headings":"Colors","what":"customColors","title":"geneviewer","text":"customColors parameter specifies colors group legend. accepts either vector colors named list direct mapping, list(\"Class1\" = \"#FF5733\", \"Class2\" = \"#33CFFF\"). Using list colors: Using named list colors; ensure color changes take effect, GC_color function call must placed function calls. example , custom_colors overwritten color settings GC_genes function. Therefore, always place GC_color function call last.","code":"# Pass a list of Colors custom_colors <- c(\"#F8766D\",\"#00BA38\",\"#619CFF\",\"#F564E3\",\"#FFC61E\",\"#00BFC4\")  GC_chart(ophA_cluster, group = \"class\", height = \"100px\") %>%   GC_color(customColors = custom_colors ) # Pass a list of Colors custom_colors <- c(\"#D62728\", \"#2CA02C\", \"#1F77B4\", \"#9467BD\", \"#FF7F0E\", \"#17BECF\")  # Create a named list of colors named_vector <- setNames(custom_colors, unique(ophA_cluster$class)) custom_colors <- as.list(named_vector)  GC_chart(ophA_cluster, group = \"class\", height = \"100px\") %>%   GC_color(customColors = custom_colors ) # Pass a list of Colors custom_colors <- c(\"#D62728\", \"#D62728\", \"#D62728\", \"#D62728\", \"#D62728\", \"#D62728\")  # Create a named list of colors named_vector <- setNames(custom_colors, unique(ophA_cluster$class)) custom_colors <- as.list(named_vector)  GC_chart(ophA_cluster, group = \"class\", height = \"100px\") %>%   GC_color(customColors = custom_colors ) %>%   GC_genes() %>%   GC_legend()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"legend","dir":"Articles","previous_headings":"","what":"Legend","title":"geneviewer","text":"GC_legend() function can used show / hide customize legend. default legend shown bottom. example shows GC_function() default settings. example advanced customization shown changing order, size, position appearance legend. color changed using GC_color function simultaneously adjusts colors legend genes.","code":"GC_chart(   ophA_clusters,    group = \"class\",    cluster = \"cluster\",   height = \"200px\") %>%  GC_legend(     show = TRUE,     position = \"bottom\", #top (left and right no supported for now)     orientation = \"horizontal\", #vertical     x = 0,     y = 0,     margin = list(top = 0, left = 50, bottom = 0,  right = 50),     width = NULL,     adjustHeight = TRUE,     order = list(),     style = list(       #backgroundColor = \"#0000\"       # Additional CSS styles     ),     positions = \"bottom\",     legendOptions = list(       cursor = \"pointer\",       colorScheme = NULL,       customColors = NULL        # Additional CSS styles     ),     legendTextOptions = list(       cursor = \"pointer\",       textAnchor = \"start\",       dy = \".35em\",       fontSize = \"12px\",       fontFamily = \"sans-serif\",       fill = \"black\"       # Additional CSS styles     )   ) GC_chart(   ophA_clusters,    group = \"class\",    cluster = \"cluster\",   height = \"200px\") %>%  GC_legend(     y = 10,     position = \"top\",     width = \"60%\",     order = sort(unique(ophA_clusters$class)),     legendTextOptions = list(       fontSize = \"14px\"     ),     legendOptions = list(stroke = \"black\", strokeWidth = \"2px\")   ) %>%    GC_color(colorScheme = \"schemePaired\")"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"scale","dir":"Articles","previous_headings":"","what":"Scale","title":"geneviewer","text":"GC_scale() function utilized adjusting chart’s scale. padding parameter can used add extra space start end cluster. visibility scale can controlled hidden parameter, , set TRUE, hides axis. y parameter can used adjust horizontal position axis (1 bottom 100 top).","code":"GC_chart(ophA_cluster, group = \"class\", height = \"100px\") %>%   GC_scale(     padding = 2,     hidden = FALSE,     axisType = \"bottom\",     y = NULL) %>%    GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"automatic-scale-breaks","dir":"Articles","previous_headings":"Scale","what":"Automatic Scale Breaks","title":"geneviewer","text":"GC_scale() function, parameters scale_breaks, scale_break_threshold, scale_break_padding can used avoid issues widely spaced genes within cluster. Setting scale_breaks TRUE introduces breaks genomic scale avoid long empty stretches. scale_break_threshold defines spacing percentage genes needed activate breaks. scale_break_padding controls padding around breaks. given example, scale break introduced cases intergenic region exceeds 20% total range gene cluster. Additionally, padding 1% added left right sides break.","code":"# With scale breaks GC_chart(ophA_cluster, group = \"class\", height = \"100px\") %>%   GC_scale(     scale_breaks = TRUE,     scale_break_threshold = 20,     scale_break_padding = 1   ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"manual-scale-adjustments","dir":"Articles","previous_headings":"Scale","what":"Manual Scale Adjustments","title":"geneviewer","text":"default minimum maximum genes start end positions used position genes along sequence. use start end parameters, values can adjusted. Scale breaks can added manually using breaks parameter. provided example range altered providing custom start end values. Additionally, scale break introduced remove extensive intergenic region exists gene 2 gene 3.","code":"GC_chart(   ophA_cluster,    start = \"start\",    end = \"end\",    group = \"class\",    height = \"100px\") %>%   GC_scale(     start = 1522,      end = 22484,     breaks =        list(         list(start = 5486, end = 9336)       )     ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"reverse-scale","dir":"Articles","previous_headings":"Scale","what":"Reverse Scale","title":"geneviewer","text":"scale can reversed setting reverse = TRUE.","code":"GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"200px\") %>%   GC_scale(cluster = 1, reverse = FALSE, ticksCount = 10) %>%   GC_scale(cluster = 2, reverse = TRUE, ticksCount = 10)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"shared-genomic-scale","dir":"Articles","previous_headings":"Scale","what":"Shared genomic scale","title":"geneviewer","text":"setting axis_type range, can standardize axis across clusters, shifting precise genomic coordinates unified scale. scale based widest span observed among clusters, starting 0 extending endpoint cluster covering largest range. Warning: using shared axis options like setting breaks reversing scale might work anymore.","code":"GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"200px\") %>%   GC_scale(axis_type = \"range\")"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"styling-1","dir":"Articles","previous_headings":"Scale","what":"Styling","title":"geneviewer","text":"scale can styled using tickStyle, textStyle lineStyle options. can pass valid CSS styles respective styling list(). amount ticks can specified using ticksCount option. Alternatively, ticks can manually specified using tickValues parameter. ticksFormat parameter used define numerical labels tick marks formatted (see: link).","code":"GC_chart(ophA_cluster, group = \"class\", height = \"100px\") %>%   GC_scale(     ticksFormat = \".2s\", # Default: \",.0f\"     tickValues = c(ophA_cluster$start, ophA_cluster$end),     #ticksCount = 10,     tickStyle =        list(         stroke = \"black\",          strokeWidth = 2,          lineLength = 12         # Any other CSS styles         ),     textStyle =        list(         y = 15,         fill = \"black\",          fontSize = \"8px\",          fontFamily = \"Arial\"         # Any other CSS styles         ),     lineStyle = list(       stroke = \"black\",        strokeWidth = 2       # Any other CSS styles       )   ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"coordinates","dir":"Articles","previous_headings":"","what":"Coordinates","title":"geneviewer","text":"Gene coordinates can displayed GC_coordinates() function. overlapping coordinates occur, , default, shifted top axis clearer visualization. default overlapThreshold parameter set 20. style ticks text can customized using tickStyle textStyle variables. scale can changed using GC_scale() function. instance want use reverse scale displaying coordinates can set GC_scale hidden. default, start end positions gene indicated coordinates. However, can customize providing values top bottom ticks, using tickValuesTop tickValuesBottom options. ticksFormat parameter used define numerical labels tick marks formatted (see: link).","code":"dbophA_cluster <- subset(ophA_clusters, cluster == \"dbophA\")  GC_chart(dbophA_cluster, group = \"class\",height = \"100px\") %>%   GC_coordinates(   rotate = -45,   yPositionTop = 55,   yPositionBottom = 45,   overlapThreshold = 20   ) %>%   GC_legend(FALSE) GC_chart(dbophA_cluster, group = \"class\",height = \"100px\") %>%   GC_scale(hidden = TRUE, reverse = TRUE) %>%   GC_coordinates(    tickStyle = list(stroke = \"grey\", strokeWidth = 1, lineLength = 10),    textStyle = list(fill = \"gray\", fontSize = \"10px\", fontFamily = \"Arial\", cursor = \"default\")    ) %>%    GC_legend(FALSE) GC_chart(dbophA_cluster, group = \"class\",height = \"100px\") %>%   GC_coordinates(     tickValuesTop = c(27371, 28937),     tickValuesBottom = c(25288, 27217),     ticksFormat = \".2s\", # Default: \",.0f\"    ) %>%    GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"scalebar","dir":"Articles","previous_headings":"","what":"Scalebar","title":"geneviewer","text":"scalebar can added gene cluster chart using GC_scaleBar(). function, default, displays scale bar 1000 base pairs (bp) labeled “1kb”. scalebar’s position label can customized using x, y, labelPosition parameters. CSS styles can added modify labels. appearance scalebar line ticks adjustable scaleBarLine scaleBarTick options.","code":"GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_scaleBar(     title = \"1kb\",     scaleBarUnit = 1000     ) %>%   GC_legend(FALSE) GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_scaleBar(     title = \"1kb\",     scaleBarUnit = 1000,     cluster = NULL,     x = 0,     y = 0,     labelStyle = list(       labelPosition = \"left\",       fontSize = \"10px\",       fontFamily = \"sans-serif\",       fill = \"black\",           cursor = \"default\"        # Any other CSS style for the label     ),     textPadding = 2,     scaleBarLineStyle = list(       stroke = \"black\",       strokeWidth = 1       # Any other CSS style for the line     ),     scaleBarTickStyle = list(       stroke = \"black\",       strokeWidth = 1          # Any other CSS style for the tick     )   ) %>%    GC_legend(y = 10) # Increase space"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"tooltip","dir":"Articles","previous_headings":"","what":"Tooltip","title":"geneviewer","text":"default, tooltip gene chart displays start end positions gene hovering . positions dynamically replaced actual start end data values gene. can customize text tooltip using formatter variable. example , tooltip customized include gene’s start end positions also name. gene name pulled ‘name’ column data set.","code":"GC_chart(ophA_cluster, group = \"class\", height = \"150px\") %>%   GC_tooltip(     formatter = \"Gene: <\/b>{name}
Start:<\/b> {start}
End:<\/b> {end}\",   ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"saving-plots","dir":"Articles","previous_headings":"","what":"Saving Plots","title":"geneviewer","text":"can save plots directly browser PNG images using save button appears hovering graph. option can disabled setting save_button parameter FALSE GC_chart function. save plots different formats, can use webshot2 package illustrated :","code":"library(webshot2)  # Generate plot with width and height specifications cluster_plot <-    GC_chart(ophA_clusters,             group = \"class\",             cluster = \"cluster\",            width = \"400px\",            height = \"250px\")  # Save plot to temp.html file htmlwidgets::saveWidget(cluster_plot, \"temp.html\", selfcontained = TRUE)  # Save plot to .png (or .jpg, .jpeg, .webp, .pdf) webshot2::webshot(   \"temp.html\",    \"output.png\",    zoom = 1, # Increase zoom for higher resolution   selector = \".geneviewer\")"},{"path":"https://nvelden.github.io/geneviewer/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Niels van der Velden. Maintainer.","code":""},{"path":"https://nvelden.github.io/geneviewer/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"van der Velden N (2024). geneviewer: Gene Cluster Visualizations R. R package version 0.1.8, https://github.com/nvelden/geneviewer.","code":"@Manual{,   title = {geneviewer: Gene Cluster Visualizations in R},   author = {Niels {van der Velden}},   year = {2024},   note = {R package version 0.1.8},   url = {https://github.com/nvelden/geneviewer}, }"},{"path":"https://nvelden.github.io/geneviewer/index.html","id":"geneviewer","dir":"","previous_headings":"","what":"geneviewer","title":"Gene Cluster Visualizations in R","text":"geneviewer R package plotting gene clusters transcripts. imports data GenBank, FASTA, GFF files, performs BlastP MUMmer alignments, displays results gene arrow maps. package offers extensive customization options, including legends, labels, annotations, scales, colors, tooltips, . explore features visit package website.","code":""},{"path":"https://nvelden.github.io/geneviewer/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Gene Cluster Visualizations in R","text":"geneviewer still development stage might lead breaking changes thus yet released CRAN. can install development version GitHub :","code":"# install.packages(\"devtools\") devtools::install_github(\"nvelden/geneviewer\")"},{"path":"https://nvelden.github.io/geneviewer/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Gene Cluster Visualizations in R","text":"example demonstrates using geneviewer plot gene cluster genomic sequence, using start end positions gene. genes grouped class labels added using GC_labels function.","code":"library(geneviewer)  # Data gene_cluster <- data.frame(   name = c(\"ophB1\", \"ophC\", \"ophA\", \"ophD\", \"ophB2\", \"ophP\", \"ophE\"),   start = c(2522, 5286, 9536, 12616, 13183, 19346, 20170),   end = c(4276, 4718, 10904, 11859, 15046, 16016, 21484),   class = c(\"Monooxygenase\", \"NTF2-like\", \"Methyltransferase\",    \"O-acyltransferase\", \"Monooxygenase\", \"Prolyloligopeptidase\",    \"F-box/RNHI-like\") )  # Chart GC_chart(gene_cluster, group = \"class\", height = \"100px\") %>%   GC_labels(\"name\")"},{"path":"https://nvelden.github.io/geneviewer/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Gene Cluster Visualizations in R","text":"additional examples corresponding code create plots, please visit Examples section.","code":""},{"path":"https://nvelden.github.io/geneviewer/index.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Gene Cluster Visualizations in R","text":"encounter issues feature requests, please open Issue.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/BRCA1_splice_variants.html","id":null,"dir":"Reference","previous_headings":"","what":"BRCA1 Splice Variants — BRCA1_splice_variants","title":"BRCA1 Splice Variants — BRCA1_splice_variants","text":"dataset contains detailed information five different splice variants BRCA1 gene. includes data types transcript features (exon, intron, UTR), chromosomal positions, strand orientations, transcript lengths.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/BRCA1_splice_variants.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BRCA1 Splice Variants — BRCA1_splice_variants","text":"","code":"BRCA1_splice_variants"},{"path":"https://nvelden.github.io/geneviewer/reference/BRCA1_splice_variants.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"BRCA1 Splice Variants — BRCA1_splice_variants","text":"data frame 119 observations 6 variables: ensembl_transcript_id Unique Ensembl transcript identifiers. character vector. type Type transcript feature, indicating whether \"exon\", \"UTR\". character vector. start start position feature chromosome. numeric vector. end end position feature chromosome. numeric vector. strand strand orientation feature, -1 indicating reverse strand. integer vector. transcript_length total length transcript base pairs. integer vector.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/BRCA1_splice_variants.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"BRCA1 Splice Variants — BRCA1_splice_variants","text":"Derived Ensembl website","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_align.html","id":null,"dir":"Reference","previous_headings":"","what":"Align gene clusters — GC_align","title":"Align gene clusters — GC_align","text":"function aligns clusters based specified gene id.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_align.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Align gene clusters — GC_align","text":"","code":"GC_align(GC_chart, id_column, id, align = \"left\")"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_align.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Align gene clusters — GC_align","text":"GC_chart chart object containing genomic data along clustering information. id_column name column contains gene identifiers. id specific identifier gene aligned. align alignment method gene. Valid values \"left\", \"right\", \"center\". Defaults \"left\".","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_align.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Align gene clusters — GC_align","text":"modified `GC_chart` object updated genomic coordinates.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_align.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Align gene clusters — GC_align","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5'),   group = c('A', 'B', 'C', 'C', 'A'),   cluster =  c(1, 1, 1, 2, 2) )   GC_chart(genes_data, group = \"group\", cluster = \"cluster\", height = \"150px\") %>%   GC_align(\"group\", \"A\", align = \"left\") %>%   GC_legend(FALSE)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"150px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"group\":[\"A\",\"B\",\"C\",\"C\",\"A\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"backgroundColor\":\"#0000\"},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90,130],\"end\":[40,120,160],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"B\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":75,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":160,\"start\":-50,\"end\":160},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[170,210],\"end\":[200,240],\"name\":[\"Gene 4\",\"Gene 5\"],\"group\":[\"C\",\"A\"],\"cluster\":[\"2\",\"2\"],\"rowID\":[4,5],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":75,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":170,\"xMax\":240,\"start\":170,\"end\":310},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Annotations to a GC_chart — GC_annotation","title":"Add Annotations to a GC_chart — GC_annotation","text":"function adds annotations specified clusters within GC chart. Annotations can various types positioned based provided coordinates. types annotations available : text, textMarker, line, arrow, symbol, rectangle, promoter, terminator.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Annotations to a GC_chart — GC_annotation","text":"","code":"GC_annotation(GC_chart, type = \"textAnnotation\", cluster = NULL, ...)"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Annotations to a GC_chart — GC_annotation","text":"GC_chart GC chart object annotations added. type Character vector specifying type annotations add. default \"text\". cluster Numeric character vector specifying clusters annotations added. ... Additional parameters customization annotations, depending type.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_annotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Annotations to a GC_chart — GC_annotation","text":"Updated GC chart object added annotations.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/reference/GC_annotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Annotations to a GC_chart — GC_annotation","text":"","code":"genes_data <- data.frame(   start = c(10, 50, 90, 130, 170, 210),   end = c(40, 80, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 1, 2, 2, 2) )  # Adding annotations to a GC chart GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"220px\") %>%   GC_annotation(     type = \"textMarker\",     cluster = 1,     position = 24,     text = \"Gene 1\",     arrowSize = 8   ) %>%   GC_annotation(     type = \"text\",     text = \"feature 1\",     x = 91,     y = 71   ) %>%   GC_annotation(     type = \"symbol\",     symbol = \"triangle\",     x = 95,     y = 64,     size = 10,     rotation = 180   ) %>%   GC_annotation(     type = \"terminator\",     x = 81   ) %>%   GC_annotation(     type = \"promoter\",     x = 49   ) %>%   # Convenience function to track mouse position on hoover   GC_trackMouse()  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"220px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":110,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[{\"type\":\"textMarker\",\"position\":24,\"text\":\"Gene 1\",\"arrowSize\":8},{\"type\":\"text\",\"text\":\"feature 1\",\"x\":91,\"y\":71},{\"type\":\"symbol\",\"symbol\":\"triangle\",\"x\":95,\"y\":64,\"size\":10,\"rotation\":180},{\"type\":\"terminator\",\"x\":81},{\"type\":\"promoter\",\"x\":49}],\"trackMouse\":{\"show\":true},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":110,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[{\"type\":\"text\",\"text\":\"feature 1\",\"x\":91,\"y\":71},{\"type\":\"symbol\",\"symbol\":\"triangle\",\"x\":95,\"y\":64,\"size\":10,\"rotation\":180},{\"type\":\"terminator\",\"x\":81},{\"type\":\"promoter\",\"x\":49}],\"trackMouse\":{\"show\":true},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_chart.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a GC Chart Visualization — GC_chart","title":"Create a GC Chart Visualization — GC_chart","text":"Generates interactive GC chart genomic data.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_chart.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a GC Chart Visualization — GC_chart","text":"","code":"GC_chart(   data,   start = \"start\",   end = \"end\",   cluster = NULL,   group = NULL,   strand = NULL,   width = \"100%\",   height = \"400px\",   style = list(),   elementId = NULL,   save_button = TRUE )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_chart.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a GC Chart Visualization — GC_chart","text":"data Data frame containing genomic information file path folder containing `.gbk` files. providing file path, data loaded processed data frame internally. start Column name indicates start positions. Default \"start\". end Column name indicates end positions. Default \"end\". cluster Optional column name used clustering purposes. Default NULL. group Column name used gene grouping influence color aesthetics. strand Optional column name indicating strand orientation. Acceptable values include 1, 'forward', 'sense', '+' represent forward strand, -1, 0, 'reverse', 'antisense', \"complement\" '-' represent reverse strand. Default NULL, meaning strand information used. width Width specification chart, '100%' 500. Default unspecified. height Height specification chart, '400px' 300. Default unspecified. style list CSS styles applied chart container. element list valid CSS property-value pair. example, list(backgroundColor = \"white\", border = \"2px solid black\"). Default empty list. elementId Optional identifier string widget. Default NULL. save_button Logical, whether include save button. Default TRUE.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_chart.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a GC Chart Visualization — GC_chart","text":"GC chart widget.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_chart.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a GC Chart Visualization — GC_chart","text":"","code":"genes_data <- data.frame(   start = c(10, 50, 90, 130, 170, 210),   end = c(40, 80, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 1, 2, 2, 2) ) # Load from data.frame GC_chart(genes_data, group = \"group\", cluster = \"cluster\", height = \"200px\") %>% GC_labels(\"name\")  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Load from folder containing .gbk files # file_path <- \"~/path/to/folder/\" # GC_chart(file_path) %>%"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_cluster.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify Cluster Settings — GC_cluster","title":"Modify Cluster Settings — GC_cluster","text":"function can switch prevention gene overlap , adjust spacing tracks alter styling specified clusters.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_cluster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify Cluster Settings — GC_cluster","text":"","code":"GC_cluster(   GC_chart,   separate_strands = NULL,   strand_spacing = NULL,   prevent_gene_overlap = NULL,   overlap_spacing = NULL,   cluster = NULL,   style = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_cluster.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify Cluster Settings — GC_cluster","text":"GC_chart gene chart object modified. separate_strands Logical, indicating whether vertically separate forward reverse genes. strand_spacing Numeric, specifies spacing genes different strands. Used `separate_strands` TRUE. prevent_gene_overlap Logical, indicating whether vertically separate overlapping genes. overlap_spacing Numeric, specifies spacing overlapping genes Used `prevent_gene_overlap` TRUE. cluster Optional; used specify clusters chart tooltips. style list CSS styles applied gene track. element list valid CSS property-value pair. example, list(backgroundColor = \"red\", color = \"white\"). ... Additional arguments passed underlying functions.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_cluster.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify Cluster Settings — GC_cluster","text":"Returns modified gene chart object.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_cluster.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Modify Cluster Settings — GC_cluster","text":"","code":"genes_data <- data.frame(   start = c(1, 10, 200, 220, 600),   end = c(10, 150, 180, 400, 400),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5'),   group = c('A', 'A', 'A', 'A', 'A') )   GC_chart(genes_data, group = \"group\", height = \"150px\") %>%   GC_cluster(separate_strands=TRUE, strand_spacing = 0) %>%   GC_legend(FALSE)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"150px\",\"save_button\":true},\"data\":{\"start\":[1,10,200,220,600],\"end\":[10,150,180,400,400],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"group\":[\"A\",\"A\",\"A\",\"A\",\"A\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"reverse\",\"forward\",\"reverse\"]},\"group\":\"group\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"backgroundColor\":\"#0000\"},\"saveButton\":true,\"series\":{\"cluster\":{\"clusterName\":\"cluster\",\"data\":{\"start\":[1,10,200,220,600],\"end\":[10,150,180,400,400],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"group\":[\"A\",\"A\",\"A\",\"A\",\"A\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"reverse\",\"forward\",\"reverse\"],\"cluster\":[\"cluster\",\"cluster\",\"cluster\",\"cluster\",\"cluster\"]},\"cluster\":{\"separateStrands\":true,\"strandSpacing\":0},\"container\":{\"height\":150,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":1,\"xMax\":600},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterFooter.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Footer to Each Cluster in a GC Chart — GC_clusterFooter","title":"Add a Footer to Each Cluster in a GC Chart — GC_clusterFooter","text":"function allows add footer specific clusters within GC chart. can specify titles, subtitles, control display styling.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterFooter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Footer to Each Cluster in a GC Chart — GC_clusterFooter","text":"","code":"GC_clusterFooter(   GC_chart,   title = NULL,   subtitle = NULL,   height = NULL,   show = TRUE,   cluster = NULL,   subtitleFont = list(),   titleFont = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterFooter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Footer to Each Cluster in a GC Chart — GC_clusterFooter","text":"GC_chart GC chart object footers added . title Character vector NULL. title displayed footer. Multiple titles can provided different clusters, recycled clusters titles. Default NULL. subtitle Character vector NULL. Subtitles accompany main titles. Default NULL. height Character vector NULL. height footer, can vary clusters. Default NULL. show Logical vector. Controls visibility footer. Default TRUE clusters. cluster Numeric character vector specifying clusters footers added updated. NULL, clusters updated. Default NULL. subtitleFont List, styling options subtitle. titleFont List, styling options title. ... Additional arguments customization footers.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterFooter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a Footer to Each Cluster in a GC Chart — GC_clusterFooter","text":"GC chart object updated footer settings specified cluster.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterFooter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Footer to Each Cluster in a GC Chart — GC_clusterFooter","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 2, 2, 2) )  # Add a simple footer with subtitle to all clusters GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"300px\") %>%   GC_clusterFooter(     title = \"Cluster Footer\",     subtitle = \"Cluster subtitle\"   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"300px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":150,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":{\"title\":\"Cluster Footer\",\"subtitle\":\"Cluster subtitle\",\"show\":true,\"subtitleFont\":[],\"titleFont\":[]},\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"},\"grid\":{\"bottom\":\"20px\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":150,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":{\"title\":\"Cluster Footer\",\"subtitle\":\"Cluster subtitle\",\"show\":true,\"subtitleFont\":[],\"titleFont\":[]},\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"},\"grid\":{\"bottom\":\"20px\"}}}},\"evals\":[],\"jsHooks\":[]}# Add styling to the title and sub title GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"300px\") %>%   GC_clusterFooter(     title = \"This is a footer\",     subtitle = \"Subtitle for the footer\",     height = \"15px\",     spacing = 15,     show = TRUE,     cluster = 1,     x = 6,     y = -20,     align = \"center\", # left / right     spacing = 12,     titleFont = list(       fontSize = \"12px\",       fontWeight = \"bold\",       fontFamily = \"sans-serif\",       fill = \"black\",       cursor = \"default\"     ),     subtitleFont = list(       fill = \"grey\",       fontSize = \"10px\",       fontStyle = \"normal\",       fontFamily = \"sans-serif\",       cursor = \"default\"     )   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"300px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":150,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":{\"title\":\"This is a footer\",\"subtitle\":\"Subtitle for the footer\",\"show\":true,\"subtitleFont\":{\"fill\":\"grey\",\"fontSize\":\"10px\",\"fontStyle\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\"},\"titleFont\":{\"fontSize\":\"12px\",\"fontWeight\":\"bold\",\"fontFamily\":\"sans-serif\",\"fill\":\"black\",\"cursor\":\"default\"},\"spacing\":15,\"x\":6,\"y\":-20,\"align\":\"center\"},\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"},\"grid\":{\"bottom\":\"15px\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":150,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterLabel.html","id":null,"dir":"Reference","previous_headings":"","what":"Set or Update Cluster Labels for a GC Chart — GC_clusterLabel","title":"Set or Update Cluster Labels for a GC Chart — GC_clusterLabel","text":"function allows set update labels specified clusters within GC chart. provides flexibility terms title, visibility, width, position, additional customization options.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterLabel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set or Update Cluster Labels for a GC Chart — GC_clusterLabel","text":"","code":"GC_clusterLabel(   GC_chart,   title = NULL,   show = TRUE,   width = \"100px\",   cluster = NULL,   position = \"left\",   wrapLabel = TRUE,   wrapOptions = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterLabel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set or Update Cluster Labels for a GC Chart — GC_clusterLabel","text":"GC_chart GC chart object. title Character vector. title cluster label. Default NULL. show Logical. Whether show cluster label. Default TRUE. width Character. width cluster label. Default \"100px\". cluster Numeric character vector. Clusters GC chart update. Default NULL. position Character. Position label, either \"left\" \"right\". Default \"left\". wrapLabel Logical. Indicates whether label wrapped. Default TRUE. wrapOptions List. Specifies wrapping options. Default empty List. ... Additional customization arguments cluster label, 'fontSize', 'fontStyle', 'fontWeight', 'fontFamily', 'cursor', etc.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterLabel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set or Update Cluster Labels for a GC Chart — GC_clusterLabel","text":"Updated GC chart new modified cluster labels.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterLabel.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set or Update Cluster Labels for a GC Chart — GC_clusterLabel","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 2, 2, 2) )  # Set cluster labels GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"200px\") %>% GC_clusterLabel(title = unique(genes_data$cluster))  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"},\"margin\":{\"left\":\"100px\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":1,\"show\":true,\"wrapLabel\":true,\"wrapOptions\":[],\"position\":\"left\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":2,\"show\":true,\"wrapLabel\":true,\"wrapOptions\":[],\"position\":\"left\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Set label for a specific cluster GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"200px\") %>% GC_clusterLabel(title = \"Cluster 1\", cluster = 1)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"},\"margin\":{\"left\":\"100px\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":\"Cluster 1\",\"show\":true,\"wrapLabel\":true,\"wrapOptions\":[],\"position\":\"left\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Style labels GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"200px\") %>%   GC_clusterLabel(     title = c(\"Cluster 1\", \"Cluster 2\"),     width = \"100px\",     x = 0,     y = 0,     position = \"left\",     wrapLabel = TRUE,     wrapOptions = list(       dyAdjust = 0,       lineHeightEms = 1.05,       lineHeightSquishFactor =  1,       splitOnHyphen =  TRUE,       centreVertically = TRUE      ),     fontSize = \"12px\",     fontStyle = \"normal\",     fontWeight = \"bold\",     fontFamily = \"sans-serif\",     cursor = \"default\"   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"},\"margin\":{\"left\":\"100px\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":\"Cluster 1\",\"show\":true,\"wrapLabel\":true,\"wrapOptions\":{\"dyAdjust\":0,\"lineHeightEms\":1.05,\"lineHeightSquishFactor\":1,\"splitOnHyphen\":true,\"centreVertically\":true},\"position\":\"left\",\"x\":0,\"y\":0,\"fontSize\":\"12px\",\"fontStyle\":\"normal\",\"fontWeight\":\"bold\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":\"Cluster 2\",\"show\":true,\"wrapLabel\":true,\"wrapOptions\":{\"dyAdjust\":0,\"lineHeightEms\":1.05,\"lineHeightSquishFactor\":1,\"splitOnHyphen\":true,\"centreVertically\":true},\"position\":\"left\",\"x\":0,\"y\":0,\"fontSize\":\"12px\",\"fontStyle\":\"normal\",\"fontWeight\":\"bold\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterTitle.html","id":null,"dir":"Reference","previous_headings":"","what":"Update cluster Title of a GC Chart Cluster — GC_clusterTitle","title":"Update cluster Title of a GC Chart Cluster — GC_clusterTitle","text":"Modify cluster title subtitle specified clusters within GC chart adjust display settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterTitle.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update cluster Title of a GC Chart Cluster — GC_clusterTitle","text":"","code":"GC_clusterTitle(   GC_chart,   title = NULL,   subtitle = NULL,   subtitleFont = list(),   titleFont = list(),   show = TRUE,   height = NULL,   cluster = NULL,   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterTitle.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update cluster Title of a GC Chart Cluster — GC_clusterTitle","text":"GC_chart GC chart object. title Character vector. Titles set clusters. subtitle Character vector. Subtitles set clusters. subtitleFont List. Settings subtitle font. titleFont List. Settings title font. show Logical. Whether display title. Default TRUE. height Character. Height title (e.g., \"40px\"). cluster Numeric character vector. Clusters GC chart update. ... Additional customization arguments title subtitle.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterTitle.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update cluster Title of a GC Chart Cluster — GC_clusterTitle","text":"Updated GC chart new title settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterTitle.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update cluster Title of a GC Chart Cluster — GC_clusterTitle","text":"","code":"genes_data <- data.frame(   start = c(10, 50, 90, 130, 170, 210),   end = c(40, 80, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 1, 2, 2, 2) )  # Basic usage GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"400px\") %>% GC_labels(\"name\") %>% GC_clusterTitle(   title = \"Cluster 1 Data\",   subtitle = \"Detailed View\",   show = TRUE,   cluster = 1 )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"400px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":{\"title\":\"Cluster 1 Data\",\"subtitle\":\"Detailed View\",\"subtitleFont\":[],\"titleFont\":[],\"show\":true},\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Customizing title style GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"400px\") %>%   GC_labels(\"name\") %>%   GC_clusterTitle(     title = \"Cluster 1 Data\",     subtitle = \"Detailed View\",     show = TRUE,     cluster = 1,     x = 0,     y = 5,     align = \"center\",     spacing = 20,     titleFont = list(       fontSize = \"16px\",       fontStyle = \"normal\",       fontWeight = \"bold\",       textDecoration = \"normal\",       fontFamily = \"sans-serif\",       cursor = \"default\",       fill = \"black\"       # Any other CSS styles     ),     subtitleFont = list(       fontSize = \"14px\",       fontStyle = \"normal\",       fontWeight = \"bold\",       textDecoration = \"normal\",       fontFamily = \"sans-serif\",       cursor = \"default\",       fill = \"black\"       # Any other CSS styles     )   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"400px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":{\"title\":\"Cluster 1 Data\",\"subtitle\":\"Detailed View\",\"subtitleFont\":{\"fontSize\":\"14px\",\"fontStyle\":\"normal\",\"fontWeight\":\"bold\",\"textDecoration\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"fill\":\"black\"},\"titleFont\":{\"fontSize\":\"16px\",\"fontStyle\":\"normal\",\"fontWeight\":\"bold\",\"textDecoration\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"fill\":\"black\"},\"show\":true,\"x\":0,\"y\":5,\"align\":\"center\",\"spacing\":20},\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_color.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Color Scheme in Gene Chart — GC_color","title":"Update Color Scheme in Gene Chart — GC_color","text":"function updates color scheme legend genes gene chart.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_color.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Color Scheme in Gene Chart — GC_color","text":"","code":"GC_color(GC_chart, colorScheme = NULL, customColors = NULL)"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_color.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Color Scheme in Gene Chart — GC_color","text":"GC_chart gene chart object modified. colorScheme Optional; character NULL, name predefined color scheme apply genes.Acceptable values include D3.js's built-color schemes like \"schemeCategory10\", \"schemeAccent\", \"schemeTableau10\". customColors Either NULL, list color values, named list color values.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_color.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Color Scheme in Gene Chart — GC_color","text":"Returns gene chart object updated color settings genes.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_color.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update Color Scheme in Gene Chart — GC_color","text":"","code":"genes_data <- data.frame(   start = c(10, 50, 90, 130, 170, 210),   end = c(40, 80, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 1, 2, 2, 2) )  GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"100px\") %>%   GC_color(colorScheme = \"schemeCategory10\")  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"100px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"legendOptions\":{\"colorScheme\":\"schemeCategory10\"}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":50,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true,\"colorScheme\":\"schemeCategory10\"},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false,\"colorScheme\":\"schemeCategory10\"},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":50,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true,\"colorScheme\":\"schemeCategory10\"},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false,\"colorScheme\":\"schemeCategory10\"},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"100px\") %>%   GC_color(customColors = c(\"red\", \"orange\", \"green\"))  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"100px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"legendOptions\":{\"customColors\":[\"red\",\"orange\",\"green\"]}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":50,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true,\"customColors\":[\"red\",\"orange\",\"green\"]},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false,\"customColors\":[\"red\",\"orange\",\"green\"]},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":50,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true,\"customColors\":[\"red\",\"orange\",\"green\"]},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false,\"customColors\":[\"red\",\"orange\",\"green\"]},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"100px\") %>%   GC_color(customColors = list(A = \"yellow\", B = \"pink\", C =  \"purple\"))  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"100px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"legendOptions\":{\"customColors\":{\"A\":\"yellow\",\"B\":\"pink\",\"C\":\"purple\"}}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":50,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true,\"customColors\":{\"A\":\"yellow\",\"B\":\"pink\",\"C\":\"purple\"}},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false,\"customColors\":{\"A\":\"yellow\",\"B\":\"pink\",\"C\":\"purple\"}},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":50,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true,\"customColors\":{\"A\":\"yellow\",\"B\":\"pink\",\"C\":\"purple\"}},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false,\"customColors\":{\"A\":\"yellow\",\"B\":\"pink\",\"C\":\"purple\"}},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_coordinates.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify Coordinates in a GC Chart — GC_coordinates","title":"Modify Coordinates in a GC Chart — GC_coordinates","text":"function updates GC chart modifying coordinates settings. allows showing hiding tick values, applying custom tick values top bottom axes, supports several customizations specific clusters chart.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_coordinates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify Coordinates in a GC Chart — GC_coordinates","text":"","code":"GC_coordinates(   GC_chart,   show = TRUE,   tickValuesTop = NULL,   tickValuesBottom = NULL,   ticksFormat = NULL,   tickStyle = list(),   textStyle = list(),   cluster = NULL,   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_coordinates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify Coordinates in a GC Chart — GC_coordinates","text":"GC_chart GC chart object modified. show Logical, whether show tick values . Can single value vector. tickValuesTop Numeric vector NULL, custom tick values used top cluster. NULL, default tick values used. tickValuesBottom Numeric vector NULL, custom tick values used bottom cluster. NULL, default tick values used. ticksFormat Format tick labels. Default \",.0f\". tickStyle List, styling options ticks. textStyle List, styling options text. coordinate modifications. NULL, applies clusters. cluster Numeric character vector NULL; specifies clusters generate coordinates .        NULL, labels applied clusters. Default NULL. ... Additional arguments passed coordinate options.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_coordinates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify Coordinates in a GC Chart — GC_coordinates","text":"Returns GC chart object updated coordinates.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_coordinates.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Modify Coordinates in a GC Chart — GC_coordinates","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5'),   cluster = c(1, 1, 2, 2, 2) )  # Add coordinates to all clusters GC_chart(genes_data, cluster = \"cluster\", group = \"name\", height = \"200px\") %>% GC_coordinates()  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"name\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"name\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"name\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 2\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"name\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"name\",\"show\":false},\"labels\":{\"group\":\"name\",\"show\":true},\"coordinates\":{\"show\":true,\"ticksFormat\":null,\"tickStyle\":[],\"textStyle\":[]},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"name\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"name\",\"show\":false},\"labels\":{\"group\":\"name\",\"show\":true},\"coordinates\":{\"show\":true,\"ticksFormat\":null,\"tickStyle\":[],\"textStyle\":[]},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Modify coordinates of a specific cluster GC_chart(genes_data, cluster = \"cluster\", group = \"name\", height = \"200px\") %>% GC_coordinates() %>% GC_coordinates(   cluster = 2,   show = TRUE,   tickValuesTop = c(130, 170, 210, 240),   tickValuesBottom = c(160, 200),   ticksFormat = \",.0f\", # \".2s\",   rotate = -45,   yPositionTop = 55,   yPositionBottom = 45,   overlapThreshold = 20,   tickStyle = list(   stroke = \"black\",   strokeWidth = 1,   lineLength = 6   ),   textStyle = list(   fill = \"black\",   fontSize = \"12px\",   fontFamily = \"Arial\",   cursor = \"default\"   ) )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"name\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"name\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"name\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 2\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"name\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"name\",\"show\":false},\"labels\":{\"group\":\"name\",\"show\":true},\"coordinates\":{\"show\":true,\"ticksFormat\":null,\"tickStyle\":[],\"textStyle\":[]},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"name\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"name\",\"show\":false},\"labels\":{\"group\":\"name\",\"show\":true},\"coordinates\":{\"show\":true,\"ticksFormat\":\",.0f\",\"tickStyle\":{\"stroke\":\"black\",\"strokeWidth\":1,\"lineLength\":6},\"textStyle\":{\"fill\":\"black\",\"fontSize\":\"12px\",\"fontFamily\":\"Arial\",\"cursor\":\"default\"},\"rotate\":-45,\"yPositionTop\":55,\"yPositionBottom\":45,\"overlapThreshold\":20,\"tickValuesTop\":[130,170,210,240],\"tickValuesBottom\":[160,200]},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify Gene Characteristics within a Chart — GC_genes","title":"Modify Gene Characteristics within a Chart — GC_genes","text":"function updates gene chart specific characteristics genes based given parameters. can show/hide genes, apply color scheme, assign custom colors, filter cluster, accept additional options.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify Gene Characteristics within a Chart — GC_genes","text":"","code":"GC_genes(   GC_chart,   group = NULL,   marker = NULL,   marker_size = NULL,   show = TRUE,   colorScheme = NULL,   customColors = NULL,   cluster = NULL,   itemStyle = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify Gene Characteristics within a Chart — GC_genes","text":"GC_chart gene chart object modified. group Column name used gene grouping influence color aesthetics. marker Character NULL, type marker represent genes chart. Allowed values 'arrow', 'boxarrow', 'box', 'cbox', 'rbox'. marker_size Character NULL, size category marker ('small', 'medium', 'large'). show Logical, whether show genes . colorScheme Character NULL, name color scheme use. customColors List NULL, custom colors apply genes. cluster Numeric character, specific cluster filter genes . itemStyle List, list styles apply individual items chart. ... Additional arguments passed gene options.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify Gene Characteristics within a Chart — GC_genes","text":"Returns modified gene chart object.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Modify Gene Characteristics within a Chart — GC_genes","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 2, 2, 2) )  # Change the appearance of a specific gene cluster GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"200px\") %>%   GC_genes(     group = \"group\",     show = TRUE,     marker = \"arrow\",     marker_size = \"medium\",     colorScheme = NULL, # One of D3.js build in colorSchemes                         # (eg. \"schemeCategory10\",                         # \"schemeAccent\", \"schemeTableau10\")     customColors = NULL, # A vector of color names     prevent_overlap = FALSE,     gene_overlap_spacing = 40,     cluster = 1, # Specify a specific cluster     x = 1,     y = 50,     stroke = \"black\",     strokeWidth = 1,     arrowheadWidth = NULL,     arrowheadHeight = NULL,     arrowHeight = NULL,     markerHeight = NULL # overwrites marker_size    )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"marker\":\"arrow\",\"markerSize\":\"medium\",\"show\":true,\"prevent_overlap\":false,\"gene_overlap_spacing\":40,\"x\":1,\"y\":50,\"stroke\":\"black\",\"strokeWidth\":1},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Change the appearance of a specific gene GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"200px\") %>% GC_genes(   cluster = 2,   itemStyle = list(list(index = 2, fill = \"red\", stroke = \"blue\")   )  )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true,\"itemStyle\":[{\"index\":2,\"fill\":\"red\",\"stroke\":\"blue\"}]},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_grid.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Grid Display of a GC Chart Cluster — GC_grid","title":"Update Grid Display of a GC Chart Cluster — GC_grid","text":"Modify grid display specified clusters within GC chart. function allows users adjust margins, width, height grid cluster.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_grid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Grid Display of a GC Chart Cluster — GC_grid","text":"","code":"GC_grid(   GC_chart,   margin = NULL,   width = NULL,   height = NULL,   direction = \"column\",   cluster = NULL )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_grid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Grid Display of a GC Chart Cluster — GC_grid","text":"GC_chart GC chart object. margin list specifying top, right, bottom, left margins. width Numeric character. Width grid. numeric, considered percentage. height Numeric. Height grid. direction Character. Layout direction grid, either \"column\" (default) vertical \"row\" horizontal. cluster Numeric character vector. Clusters GC chart update.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_grid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Grid Display of a GC Chart Cluster — GC_grid","text":"Updated GC chart new grid display settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_grid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update Grid Display of a GC Chart Cluster — GC_grid","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 2, 2, 2) )  # Set Margin of clusters GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"200px\") %>% GC_grid(margin = list(left = \"50px\", right = \"0px\"))  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"},\"margin\":{\"left\":\"50px\",\"right\":\"0px\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"50px\",\"right\":\"0px\"}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"50px\",\"right\":\"0px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"50px\",\"right\":\"0px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Set height of a specific cluster GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"200px\") %>% GC_grid(height = \"120px\", cluster = 2)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":120,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Labels to Each Cluster in a GC Chart — GC_labels","title":"Add Labels to Each Cluster in a GC Chart — GC_labels","text":"function adds labels cluster within GC chart. provides option show hide labels supports customization label properties. can automatically pick group names labels `GC_chart` object provided.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Labels to Each Cluster in a GC Chart — GC_labels","text":"","code":"GC_labels(   GC_chart,   label = NULL,   show = TRUE,   cluster = NULL,   itemStyle = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Labels to Each Cluster in a GC Chart — GC_labels","text":"GC_chart `GC chart` object labels added. label Character vector, logical, NULL. Specific labels clusters. NULL `GC_chart` group names, used labels. show Logical; controls visibility labels. Default `TRUE`. cluster Numeric character vector NULL; specifies clusters labeled. NULL, labels applied clusters. Default NULL. itemStyle List, list styles apply individual items chart. ... Additional arguments customization labels.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Labels to Each Cluster in a GC Chart — GC_labels","text":"`GC chart` object updated label settings specified cluster.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Labels to Each Cluster in a GC Chart — GC_labels","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 2, 2, 2) )  # Add labels to all clusters GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"200px\") %>% GC_labels()  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Add labels and styling GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"200px\") %>% GC_labels(  label = \"group\",  show = TRUE,  x = 0,  y = 50,  dy = \"-1.2em\",  dx = \"0em\",  rotate = 0,  adjustLabels = TRUE, # Rotate labels to prevent overlap  fontSize = \"12px\",  fontStyle = \"italic\",  fill = \"black\",  fontFamily = \"sans-serif\",  textAnchor = \"middle\",  cursor = \"default\", )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"group\",\"x\":0,\"y\":50,\"dy\":\"-1.2em\",\"dx\":\"0em\",\"rotate\":0,\"adjustLabels\":true,\"fontSize\":\"12px\",\"fontStyle\":\"italic\",\"fill\":\"black\",\"fontFamily\":\"sans-serif\",\"textAnchor\":\"middle\",\"cursor\":\"default\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"group\",\"x\":0,\"y\":50,\"dy\":\"-1.2em\",\"dx\":\"0em\",\"rotate\":0,\"adjustLabels\":true,\"fontSize\":\"12px\",\"fontStyle\":\"italic\",\"fill\":\"black\",\"fontFamily\":\"sans-serif\",\"textAnchor\":\"middle\",\"cursor\":\"default\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Alter style of a specific label GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"200px\") %>% GC_labels(label = \"group\") %>% GC_labels(   cluster = 1,   itemStyle = list(     list(index = 0, fill = \"red\", fontSize = \"14px\", fontWeight = \"bold\")   ) )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"group\",\"itemStyle\":[{\"index\":0,\"fill\":\"red\",\"fontSize\":\"14px\",\"fontWeight\":\"bold\"}]},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_legend.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Legend for a Gene Chart — GC_legend","title":"Set Legend for a Gene Chart — GC_legend","text":"function configures legend gene chart. allows toggling legend's visibility, setting background color, assigning custom labels legend entries. function can also handle additional customizations various options.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_legend.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Legend for a Gene Chart — GC_legend","text":"","code":"GC_legend(   GC_chart,   group = NULL,   show = TRUE,   backgroundColor = \"#0000\",   order = list(),   position = \"bottom\",   style = list(),   legendOptions = list(),   legendTextOptions = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_legend.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Legend for a Gene Chart — GC_legend","text":"GC_chart gene chart object modified. group Optional; character NULL, specifies groups include legend. NULL, groups taken 'group' attribute 'GC_chart' object. show Logical, specifies whether display legend. backgroundColor String, background color legend. order Optional; list, specifies order legend labels. position Character. Position legend, either \"top\" \"bottom\". Default \"bottom\". style list CSS styles applied chart container. element list valid CSS property-value pair. example, list(backgroundColor = \"white\", border = \"2px solid black\"). Default empty list. legendOptions List, additional options legend. legendTextOptions List, additional text options legend. ... Additional arguments passed legend configuration.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_legend.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Legend for a Gene Chart — GC_legend","text":"Returns modified gene chart object legend configured.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_legend.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set Legend for a Gene Chart — GC_legend","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'B', 'B', 'A', 'C'),   cluster = c('A', 'A', 'A', 'B', 'B') )  # Customize legend GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"200px\") %>%   GC_legend(     position = \"top\", #bottom     orientation = \"horizontal\", #vertical     x = 0,     y = 0,     width = NULL, # 100 / \"100px\" / 50%     adjustHeight = TRUE,     backgroundColor = \"#0000\",     order = list(),     positions = \"bottom\",     style = list(       backgroundColor = \"#0000\"       # Any other CSS styles     ),     legendOptions = list(       cursor = \"pointer\",       colorScheme = NULL,       customColors = NULL # c(\"red\", \"green\", \"orange\")       # Additional styles     ),     legendTextOptions = list(       cursor = \"pointer\",       textAnchor = \"start\",       dy = \".35em\",       fontSize = \"12px\",       fontFamily = \"sans-serif\",       fill = \"black\"       # Additional styles     )   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"A\",\"A\",\"A\",\"B\",\"B\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"top\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":\"#0000\"},\"backgroundColor\":\"#0000\",\"legendOptions\":{\"cursor\":\"pointer\",\"colorScheme\":null,\"customColors\":null},\"legendTextOptions\":{\"cursor\":\"pointer\",\"textAnchor\":\"start\",\"dy\":\".35em\",\"fontSize\":\"12px\",\"fontFamily\":\"sans-serif\",\"fill\":\"black\"},\"orientation\":\"horizontal\",\"x\":0,\"y\":0,\"adjustHeight\":true,\"positions\":\"bottom\"},\"saveButton\":true,\"series\":{\"A\":{\"clusterName\":\"A\",\"data\":{\"start\":[10,90,130],\"end\":[40,120,160],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\"],\"group\":[\"A\",\"B\",\"B\"],\"cluster\":[\"A\",\"A\",\"A\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":160},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"B\":{\"clusterName\":\"B\",\"data\":{\"start\":[170,210],\"end\":[200,240],\"name\":[\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"C\"],\"cluster\":[\"B\",\"B\"],\"rowID\":[4,5],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":170,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_links.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Links to GC Chart — GC_links","title":"Add Links to GC Chart — GC_links","text":"Add links generated `get_links` `GC_chart` object. Links added graph respective rowIDs.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_links.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Links to GC Chart — GC_links","text":"","code":"GC_links(   GC_chart,   group = NULL,   data = NULL,   value1 = NULL,   value2 = NULL,   cluster = NULL,   curve = TRUE,   measure = \"identity\",   show_links = TRUE,   label = TRUE,   normal_color = \"#969696\",   inverted_color = \"#d62728\",   use_group_colors = FALSE,   color_bar = TRUE,   colorBarOptions = list(),   linkStyle = list(),   labelStyle = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_links.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Links to GC Chart — GC_links","text":"GC_chart Gene chart object. group name column data create value pairs . data data.frame containing linking data. value1 Optional vector group values generate links . value2 Optional vector group values generate links . cluster Numeric character vector NULL; specifies clusters. curve Logical; `TRUE`, links curved, otherwise straight. measure Character; specifies measure use link color intensity. \"identity\", \"similarity\", \"none\". show_links Logical; `TRUE`, links shown, otherwise hidden. label Logical; `TRUE`, shows measure labels links, otherwise hidden. normal_color Color links normal state. inverted_color Color inverted links. use_group_colors Logical; `TRUE`, color links group. color_bar Logical; `TRUE`, color bar displayed. colorBarOptions List options customize color bar appearance. linkStyle list CSS styles apply links. labelStyle list CSS styles specifically labels. ... Additional arguments passed links.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_links.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Links to GC Chart — GC_links","text":"Modified `GC_chart` object added links.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/reference/GC_links.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Links to GC Chart — GC_links","text":"","code":"# Add links between all groups in each cluster genes_data <- data.frame(   start = c(10, 90, 130, 170, 240, 250, 300, 340, 380, 420),   end = c(40, 120, 160, 200, 210, 270, 330, 370, 410, 450),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5',            'Gene 6', 'Gene 7', 'Gene 8', 'Gene 9', 'Gene 10'),   group = c('A', 'B', 'C', 'A', 'B', 'C', 'A', 'B', 'C', 'D'),   identity = c(NA, NA, NA, 50, 40, 100, 60, 65, 20, NA),   similarity = c(NA, NA, NA, 40, 30, 90, 50, 55, 10, NA),   cluster = c(1, 1, 1, 2, 2, 2, 3, 3, 3, 3) ) GC_chart(genes_data,          cluster = \"cluster\",          height = \"200px\") %>%   GC_links(     group = \"group\",     value1 = \"A\",     value2 = \"B\",     measure = \"identity\",     label = FALSE) %>%   GC_labels(label = \"group\")  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,240,250,300,340,380,420],\"end\":[40,120,160,200,210,270,330,370,410,450],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\",\"Gene 7\",\"Gene 8\",\"Gene 9\",\"Gene 10\"],\"group\":[\"A\",\"B\",\"C\",\"A\",\"B\",\"C\",\"A\",\"B\",\"C\",\"D\"],\"identity\":[null,null,null,50,40,100,60,65,20,null],\"similarity\":[null,null,null,40,30,90,50,55,10,null],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\",\"3\",\"3\",\"3\",\"3\"],\"rowID\":[1,2,3,4,5,6,7,8,9,10],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"reverse\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":null,\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90,130],\"end\":[40,120,160],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"B\",\"C\"],\"identity\":[null,null,null],\"similarity\":[null,null,null],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":160},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[170,240,250],\"end\":[200,210,270],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"C\"],\"identity\":[50,40,100],\"similarity\":[40,30,90],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"reverse\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":170,\"xMax\":270},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"3\":{\"clusterName\":\"3\",\"data\":{\"start\":[300,340,380,420],\"end\":[330,370,410,450],\"name\":[\"Gene 7\",\"Gene 8\",\"Gene 9\",\"Gene 10\"],\"group\":[\"A\",\"B\",\"C\",\"D\"],\"identity\":[60,65,20,null],\"similarity\":[50,55,10,null],\"cluster\":[\"3\",\"3\",\"3\",\"3\"],\"rowID\":[7,8,9,10],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":300,\"xMax\":450},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}},\"links\":[{\"data\":{\"cluster1\":[\"1\",\"2\"],\"group1\":[\"A\",\"A\"],\"start1\":[10,170],\"end1\":[40,200],\"cluster2\":[\"2\",\"3\"],\"group2\":[\"B\",\"B\"],\"start2\":[240,340],\"end2\":[210,370],\"identity\":[40,65],\"linkID\":[\"0-1\",\"0-2\"]},\"options\":{\"group\":\"group\",\"curve\":true,\"measure\":\"identity\",\"showLinks\":true,\"label\":false,\"normalColor\":\"#969696\",\"invertedColor\":\"#d62728\",\"useGroupColors\":false,\"value1\":\"A\",\"value2\":\"B\",\"colorBar\":true}}]},\"evals\":[],\"jsHooks\":[]} # Add links between group A of cluster 1 and A and B of cluster 2 GC_chart(genes_data,          cluster = \"cluster\",          height = \"200px\") %>%          GC_labels(label = \"group\") %>%          GC_links(group = \"group\",                    value1 = c(\"A\", \"A\"),                    value2 = c(\"B\", \"A\"),                    label = FALSE,                    cluster = c(1,2))  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,240,250,300,340,380,420],\"end\":[40,120,160,200,210,270,330,370,410,450],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\",\"Gene 7\",\"Gene 8\",\"Gene 9\",\"Gene 10\"],\"group\":[\"A\",\"B\",\"C\",\"A\",\"B\",\"C\",\"A\",\"B\",\"C\",\"D\"],\"identity\":[null,null,null,50,40,100,60,65,20,null],\"similarity\":[null,null,null,40,30,90,50,55,10,null],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\",\"3\",\"3\",\"3\",\"3\"],\"rowID\":[1,2,3,4,5,6,7,8,9,10],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"reverse\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":null,\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90,130],\"end\":[40,120,160],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"B\",\"C\"],\"identity\":[null,null,null],\"similarity\":[null,null,null],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":160},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[170,240,250],\"end\":[200,210,270],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"C\"],\"identity\":[50,40,100],\"similarity\":[40,30,90],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"reverse\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":170,\"xMax\":270},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"3\":{\"clusterName\":\"3\",\"data\":{\"start\":[300,340,380,420],\"end\":[330,370,410,450],\"name\":[\"Gene 7\",\"Gene 8\",\"Gene 9\",\"Gene 10\"],\"group\":[\"A\",\"B\",\"C\",\"D\"],\"identity\":[60,65,20,null],\"similarity\":[50,55,10,null],\"cluster\":[\"3\",\"3\",\"3\",\"3\"],\"rowID\":[7,8,9,10],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":300,\"xMax\":450},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}},\"links\":[{\"data\":{\"cluster1\":[\"1\",\"1\"],\"group1\":[\"A\",\"A\"],\"start1\":[10,10],\"end1\":[40,40],\"cluster2\":[\"2\",\"2\"],\"group2\":[\"A\",\"B\"],\"start2\":[170,240],\"end2\":[200,210],\"identity\":[50,40],\"linkID\":[\"0-1\",\"0-2\"]},\"options\":{\"group\":\"group\",\"curve\":true,\"measure\":\"identity\",\"showLinks\":true,\"label\":false,\"normalColor\":\"#969696\",\"invertedColor\":\"#d62728\",\"useGroupColors\":false,\"value1\":[\"A\",\"A\"],\"value2\":[\"B\",\"A\"],\"colorBar\":true}}]},\"evals\":[],\"jsHooks\":[]} # Style links and color bar GC_chart(genes_data,          cluster = \"cluster\",          height = \"200px\" ) %>%   GC_links(     group = \"group\",     data = NULL,     curve = TRUE,     measure = \"identity\",     show_links = TRUE,     label = TRUE,     normal_color = \"#1f77b4\",     inverted_color = \"#d62728\",     use_group_colors = FALSE,     color_bar = TRUE,     colorBarOptions = list(       x = 0,       y = 24,       width = 10,       height = 60,       labelOptions = list(         fontSize = 8,         xOffset = 2,         yOffset = 0         # Any other CSS style       ),       titleOptions = list(         fontSize = 10,         xOffset = 2,         yOffset = 0         # Any other CSS style       ),       barOptions = list(         stroke = \"#000\",         strokeWidth = 0.5,         opacity = 1         # Any other CSS style       )     ),     linkStyle = list(       stroke = \"black\",       strokeWidth = 0.5,       fillOpacity = 0.4       # Any other CSS style     ),     labelStyle = list(       fontSize = \"8px\"       # Any other CSS style     )   ) %>%   GC_labels(label = \"group\", cluster = 1) %>%   GC_clusterLabel()  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,240,250,300,340,380,420],\"end\":[40,120,160,200,210,270,330,370,410,450],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\",\"Gene 7\",\"Gene 8\",\"Gene 9\",\"Gene 10\"],\"group\":[\"A\",\"B\",\"C\",\"A\",\"B\",\"C\",\"A\",\"B\",\"C\",\"D\"],\"identity\":[null,null,null,50,40,100,60,65,20,null],\"similarity\":[null,null,null,40,30,90,50,55,10,null],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\",\"3\",\"3\",\"3\",\"3\"],\"rowID\":[1,2,3,4,5,6,7,8,9,10],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"reverse\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"},\"margin\":{\"left\":\"100px\"}},\"legend\":{\"group\":null,\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90,130],\"end\":[40,120,160],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"B\",\"C\"],\"identity\":[null,null,null],\"similarity\":[null,null,null],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":160},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":\"1\",\"show\":true,\"wrapLabel\":true,\"wrapOptions\":[],\"position\":\"left\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[170,240,250],\"end\":[200,210,270],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"C\"],\"identity\":[50,40,100],\"similarity\":[40,30,90],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"reverse\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":170,\"xMax\":270},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":\"2\",\"show\":true,\"wrapLabel\":true,\"wrapOptions\":[],\"position\":\"left\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"3\":{\"clusterName\":\"3\",\"data\":{\"start\":[300,340,380,420],\"end\":[330,370,410,450],\"name\":[\"Gene 7\",\"Gene 8\",\"Gene 9\",\"Gene 10\"],\"group\":[\"A\",\"B\",\"C\",\"D\"],\"identity\":[60,65,20,null],\"similarity\":[50,55,10,null],\"cluster\":[\"3\",\"3\",\"3\",\"3\"],\"rowID\":[7,8,9,10],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":300,\"xMax\":450},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":\"3\",\"show\":true,\"wrapLabel\":true,\"wrapOptions\":[],\"position\":\"left\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}},\"links\":[{\"data\":{\"cluster1\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"group1\":[\"A\",\"B\",\"C\",\"A\",\"B\",\"C\"],\"start1\":[10,90,130,170,240,250],\"end1\":[40,120,160,200,210,270],\"cluster2\":[\"2\",\"2\",\"2\",\"3\",\"3\",\"3\"],\"start2\":[170,240,250,300,340,380],\"end2\":[200,210,270,330,370,410],\"identity\":[50,40,100,60,65,20],\"linkID\":[\"0-1\",\"0-2\",\"0-3\",\"0-4\",\"0-5\",\"0-6\"]},\"options\":{\"group\":\"group\",\"curve\":true,\"measure\":\"identity\",\"showLinks\":true,\"label\":true,\"normalColor\":\"#1f77b4\",\"invertedColor\":\"#d62728\",\"useGroupColors\":false,\"colorBar\":true,\"colorBarOptions\":{\"x\":0,\"y\":24,\"width\":10,\"height\":60,\"labelOptions\":{\"fontSize\":8,\"xOffset\":2,\"yOffset\":0},\"titleOptions\":{\"fontSize\":10,\"xOffset\":2,\"yOffset\":0},\"barOptions\":{\"stroke\":\"#000\",\"strokeWidth\":0.5,\"opacity\":1}},\"linkStyle\":{\"stroke\":\"black\",\"strokeWidth\":0.5,\"fillOpacity\":0.4},\"labelStyle\":{\"fontSize\":\"8px\"}}}]},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_normalize.html","id":null,"dir":"Reference","previous_headings":"","what":"Normalize Gene Clusters in a Genomic Chart — GC_normalize","title":"Normalize Gene Clusters in a Genomic Chart — GC_normalize","text":"function normalizes genomic coordinates set genes within cluster, ensuring genes evenly spaced along entire range cluster. function allows option preserve original gene lengths introduce customized gaps genes.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_normalize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Normalize Gene Clusters in a Genomic Chart — GC_normalize","text":"","code":"GC_normalize(   GC_chart,   group = NULL,   cluster = NULL,   normalize = TRUE,   preserve_gene_length = TRUE,   gap = NULL,   custom_gaps = list() )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_normalize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Normalize Gene Clusters in a Genomic Chart — GC_normalize","text":"GC_chart chart object containing genomic data clustering information. chart object must include `series` component data cluster. group Column name containing gene names apply custom gaps . cluster vector cluster names normalized. `NULL`, clusters `GC_chart` normalized. normalize logical value indicating whether normalize gene positions within cluster. Default `TRUE`. preserve_gene_length logical vector indicating whether preserve original gene lengths cluster. single value provided, recycled clusters. gap numeric vector specifying proportion total length used gap genes cluster. value must 0 1. single value provided, recycled clusters. `NULL`, gaps calculated based actual spacing genes original data. custom_gaps named list name corresponds gene name value numeric factor adjust gap gene.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_normalize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Normalize Gene Clusters in a Genomic Chart — GC_normalize","text":"modified `GC_chart` object normalized gene coordinates   specified clusters.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_normalize.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Normalize Gene Clusters in a Genomic Chart — GC_normalize","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 10, 90, 130),   end = c(40, 120, 160, 40, 120, 160),   name = c('Gene 1', 'Gene 2', 'Gene 3','Gene 1', 'Gene 2', 'Gene 3'),   group = c('A', 'B', 'C', 'A', 'B', 'C'),   cluster =  c(1, 1, 1, 2, 2, 2) )  GC_chart(genes_data, group = \"group\", cluster = \"cluster\", height = \"150px\") %>%   GC_normalize(     cluster = 2,     preserve_gene_length = TRUE,     gap = NULL  )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"150px\",\"save_button\":true},\"data\":{\"rowID\":[1,2,3,4,5,6],\"start\":[10,90,130,10,60,110],\"end\":[40,120,160,40,90,140],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"B\",\"C\",\"A\",\"B\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"original_start\":[null,null,null,10,90,130],\"original_end\":[null,null,null,40,120,160]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90,130],\"end\":[40,120,160],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"B\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":75,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":160},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[10,60,110],\"end\":[40,90,140],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"B\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"],\"original_start\":[10,90,130],\"original_end\":[40,120,160]},\"cluster\":[],\"container\":{\"height\":75,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":140},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scale.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Scale of a GC Chart Cluster — GC_scale","title":"Update Scale of a GC Chart Cluster — GC_scale","text":"Modify scale settings specified clusters within GC chart.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scale.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Scale of a GC Chart Cluster — GC_scale","text":"","code":"GC_scale(   GC_chart,   cluster = NULL,   start = NULL,   end = NULL,   padding = 2,   hidden = FALSE,   breaks = list(),   tickValues = NULL,   reverse = FALSE,   axis_position = \"bottom\",   axis_type = \"position\",   y = NULL,   scale_breaks = FALSE,   scale_break_threshold = 20,   scale_break_padding = 1,   ticksCount = 10,   ticksFormat = NULL,   tickStyle = list(),   textStyle = list(),   lineStyle = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scale.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Scale of a GC Chart Cluster — GC_scale","text":"GC_chart GC chart object. cluster Numeric character vector specifying clusters GC chart update. start Numeric vector indicating starting point scale. Default NULL. end Numeric vector indicating end point scale. Default NULL. padding Numeric value percentage string indicating padding either side scale. value can number string format '2%'. Default 2. hidden Logical flag indicating whether axis hidden. Default FALSE. breaks List specifying settings scale breaks. Default empty list (). tickValues Numeric vector NULL, custom tick values used top cluster. NULL, default tick values used. reverse Logical flag indicating whether reverse scale corresponding cluster. Default FALSE. axis_position Character string indicating type axis ('top' bottom'). Default 'bottom'. axis_type Character string indicating type axis ('position' 'range'). Default 'position'. y Numeric value 1 100 indicating y-position x-axis. Default NULL. scale_breaks Logical flag indicating scale breaks employed. Default FALSE. scale_break_threshold Numeric value indicating threshold percentage determining scale breaks. Default 20. scale_break_padding Numeric value indicating padding either side scale break. Default 1. ticksCount Numeric value indicating number ticks scale. Default 10. ticksFormat Format tick labels; depends axis_type, defaulting \",.0f\" 'position' \".2s\" 'range' NULL. tickStyle List specifying style ticks. textStyle List specifying style tick text. lineStyle List specifying style axis line. ... Additional arguments scale settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scale.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Scale of a GC Chart Cluster — GC_scale","text":"Updated GC chart new scale settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scale.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update Scale of a GC Chart Cluster — GC_scale","text":"","code":"genes_data <- data.frame(   start = c(100, 1000, 2000),   end = c(150, 1500, 2500),   name = c('Gene 4', 'Gene 5', 'Gene 6'),   group = c('B', 'A', 'C'),   cluster = c(2, 2, 2) ) #Example usage with all custom options GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"200px\") %>%   GC_scale(     start = 1,     end = 2600,     padding = 2,     hidden = FALSE,     reverse = FALSE,     axis_position = \"bottom\",     # breaks = list(     #  list(start = 160, end = 900),     #  list(start = 1600, end = 1900)     # ),     # tickValues = c(1, 2600),     scale_breaks = TRUE,     scale_break_threshold = 20,     scale_break_padding = 1,     ticksCount = 10,     ticksFormat = \",.0f\",     y = NULL,     tickStyle =       list(         stroke = \"grey\",         strokeWidth = 1,         lineLength = 6         # Any other CSS styles       ),     textStyle =       list(         fill = \"black\",         fontSize = \"10px\",         fontFamily = \"Arial\",         cursor = \"default\"         # Any other CSS styles       ),     lineStyle = list(       stroke = \"grey\",       strokeWidth = 1       # Any other CSS styles     )   ) %>%   GC_legend(FALSE)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[100,1000,2000],\"end\":[150,1500,2500],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"backgroundColor\":\"#0000\"},\"saveButton\":true,\"series\":{\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[100,1000,2000],\"end\":[150,1500,2500],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"start\":1,\"end\":2600,\"xMin\":null,\"xMax\":null,\"padding\":2,\"hidden\":false,\"breaks\":[{\"start\":175.01,\"end\":974.99},{\"start\":1525.01,\"end\":1974.99}],\"tickValues\":null,\"reverse\":false,\"axisPosition\":\"bottom\",\"axisType\":\"position\",\"scale_breaks\":true,\"scale_break_threshold\":20,\"scale_break_padding\":1,\"ticksCount\":10,\"ticksFormat\":\",.0f\",\"y\":null,\"tickStyle\":{\"stroke\":\"grey\",\"strokeWidth\":1,\"lineLength\":6},\"textStyle\":{\"fill\":\"black\",\"fontSize\":\"10px\",\"fontFamily\":\"Arial\",\"cursor\":\"default\"},\"lineStyle\":{\"stroke\":\"grey\",\"strokeWidth\":1}},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scaleBar.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Scale Bar of a GC Chart Cluster — GC_scaleBar","title":"Update Scale Bar of a GC Chart Cluster — GC_scaleBar","text":"Modify scale bar settings specified clusters within GC chart.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scaleBar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Scale Bar of a GC Chart Cluster — GC_scaleBar","text":"","code":"GC_scaleBar(   GC_chart,   show = TRUE,   cluster = NULL,   scaleBarLineStyle = list(),   scaleBarTickStyle = list(),   labelStyle = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scaleBar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Scale Bar of a GC Chart Cluster — GC_scaleBar","text":"GC_chart GC chart object. show Logical. Whether show scale bar. cluster Numeric character vector. Clusters GC chart update. scaleBarLineStyle List style options scale bar line. scaleBarTickStyle List style options scale bar ticks. labelStyle List style options scale bar label. ... Additional arguments scale bar settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scaleBar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Scale Bar of a GC Chart Cluster — GC_scaleBar","text":"Updated GC chart new scale bar settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scaleBar.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update Scale Bar of a GC Chart Cluster — GC_scaleBar","text":"","code":"genes_data <- data.frame(  start = c(1000, 9000, 13000, 17000, 21000),  end = c(4000, 12000, 16000, 20000, 24000),  name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),  group = c('A', 'B', 'B', 'A', 'C'),  cluster = c(1, 1, 2, 2, 2) )  # Set scale bar for individual clusters GC_chart(genes_data, cluster =\"cluster\", group = \"group\") %>% GC_scaleBar(cluster = 1, title = \"1 kb\", scaleBarUnit = 1000) %>% GC_scaleBar(cluster = 2, title = \"2 kb\", scaleBarUnit = 2000)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"400px\",\"save_button\":true},\"data\":{\"start\":[1000,9000,13000,17000,21000],\"end\":[4000,12000,16000,20000,24000],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[1000,9000],\"end\":[4000,12000],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":1000,\"xMax\":12000},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":{\"show\":true,\"scaleBarLineStyle\":[],\"scaleBarTickStyle\":[],\"labelStyle\":[],\"title\":\"1 kb\",\"scaleBarUnit\":1000},\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[13000,17000,21000],\"end\":[16000,20000,24000],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":13000,\"xMax\":24000},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":{\"show\":true,\"scaleBarLineStyle\":[],\"scaleBarTickStyle\":[],\"labelStyle\":[],\"title\":\"2 kb\",\"scaleBarUnit\":2000},\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Style scale bar GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"400px\") %>%   GC_scaleBar(     title = \"1kb\",     scaleBarUnit = 1000,     cluster = NULL,     x = 0,     y = 50,     labelStyle = list(       labelPosition =  \"left\",       fontSize = \"10px\",       fontFamily = \"sans-serif\",       fill = \"red\", # Text color       cursor = \"default\"       # Any other CSS style for the label     ),     textPadding = -2,     scaleBarLineStyle = list(       stroke = \"black\",       strokeWidth = 1       # Any other CSS style for the line     ),     scaleBarTickStyle = list(       stroke = \"black\",       strokeWidth = 1       # Any other CSS style for the tick     )   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"400px\",\"save_button\":true},\"data\":{\"start\":[1000,9000,13000,17000,21000],\"end\":[4000,12000,16000,20000,24000],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[1000,9000],\"end\":[4000,12000],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":1000,\"xMax\":12000},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":{\"show\":true,\"scaleBarLineStyle\":{\"stroke\":\"black\",\"strokeWidth\":1},\"scaleBarTickStyle\":{\"stroke\":\"black\",\"strokeWidth\":1},\"labelStyle\":{\"labelPosition\":\"left\",\"fontSize\":\"10px\",\"fontFamily\":\"sans-serif\",\"fill\":\"red\",\"cursor\":\"default\"},\"title\":\"1kb\",\"scaleBarUnit\":1000,\"x\":0,\"y\":50,\"textPadding\":-2},\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[13000,17000,21000],\"end\":[16000,20000,24000],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":13000,\"xMax\":24000},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":{\"show\":true,\"scaleBarLineStyle\":{\"stroke\":\"black\",\"strokeWidth\":1},\"scaleBarTickStyle\":{\"stroke\":\"black\",\"strokeWidth\":1},\"labelStyle\":{\"labelPosition\":\"left\",\"fontSize\":\"10px\",\"fontFamily\":\"sans-serif\",\"fill\":\"red\",\"cursor\":\"default\"},\"title\":\"1kb\",\"scaleBarUnit\":1000,\"x\":0,\"y\":50,\"textPadding\":-2},\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_sequence.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Sequence Display of a GC Chart Cluster — GC_sequence","title":"Update Sequence Display of a GC Chart Cluster — GC_sequence","text":"Modify sequence display break markers specified clusters within GC chart.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_sequence.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Sequence Display of a GC Chart Cluster — GC_sequence","text":"","code":"GC_sequence(   GC_chart,   show = TRUE,   cluster = NULL,   y = 50,   sequenceStyle = list(),   markerStyle = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_sequence.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Sequence Display of a GC Chart Cluster — GC_sequence","text":"GC_chart GC chart object. show Logical, whether display sequence (default TRUE). cluster Numeric character vector specifying clusters update. y Vertical position sequence line (default 50). sequenceStyle list styling options sequence line. markerStyle list styling options sequence break markers. ... Additional customization arguments sequence display.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_sequence.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Sequence Display of a GC Chart Cluster — GC_sequence","text":"updated GC chart modified sequence display settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_sequence.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Update Sequence Display of a GC Chart Cluster — GC_sequence","text":"function allows customization sequence line break markers GC chart. offers options adjust sequence line (`sequenceStyle`) break markers (`markerStyle`). `y` parameter can used set vertical position sequence.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_sequence.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update Sequence Display of a GC Chart Cluster — GC_sequence","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 2, 2, 2) )  # Basic usage GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"200px\") %>% GC_labels(\"name\") %>% GC_sequence(show = TRUE, y = 50, cluster = NULL)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true,\"y\":50,\"sequenceStyle\":[],\"markerStyle\":[]},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true,\"y\":50,\"sequenceStyle\":[],\"markerStyle\":[]},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Customize sequence and marker styles GC_chart(genes_data, cluster=\"cluster\", group = \"group\", height = \"200px\") %>%   GC_scale(hidden = TRUE, scale_breaks = TRUE) %>%   GC_sequence(     start = NULL,     end = NULL,     sequenceStyle = list(       stroke = \"blue\",       strokeWidth = 1       # Any other CSS style     ),     markerStyle = list(       stroke = \"blue\",       strokeWidth = 1,       gap = 3,       tiltAmount = 5       # Any other CSS style     )   ) %>%   GC_legend(FALSE)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"backgroundColor\":\"#0000\"},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true,\"y\":50,\"sequenceStyle\":{\"stroke\":\"blue\",\"strokeWidth\":1},\"markerStyle\":{\"stroke\":\"blue\",\"strokeWidth\":1,\"gap\":3,\"tiltAmount\":5}},\"scale\":{\"start\":null,\"end\":null,\"xMin\":null,\"xMax\":null,\"padding\":2,\"hidden\":true,\"breaks\":[{\"start\":42.11,\"end\":87.89}],\"tickValues\":null,\"reverse\":false,\"axisPosition\":\"bottom\",\"axisType\":\"position\",\"scale_breaks\":true,\"scale_break_threshold\":20,\"scale_break_padding\":1,\"ticksCount\":10,\"ticksFormat\":null,\"y\":null,\"tickStyle\":[],\"textStyle\":[],\"lineStyle\":[]},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true,\"y\":50,\"sequenceStyle\":{\"stroke\":\"blue\",\"strokeWidth\":1},\"markerStyle\":{\"stroke\":\"blue\",\"strokeWidth\":1,\"gap\":3,\"tiltAmount\":5}},\"scale\":{\"start\":null,\"end\":null,\"xMin\":null,\"xMax\":null,\"padding\":2,\"hidden\":true,\"breaks\":[],\"tickValues\":null,\"reverse\":false,\"axisPosition\":\"bottom\",\"axisType\":\"position\",\"scale_breaks\":true,\"scale_break_threshold\":20,\"scale_break_padding\":1,\"ticksCount\":10,\"ticksFormat\":null,\"y\":null,\"tickStyle\":[],\"textStyle\":[],\"lineStyle\":[]},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_title.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Title to a GC_chart — GC_title","title":"Add Title to a GC_chart — GC_title","text":"Modify cluster title subtitle specified clusters within GC chart adjust display settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_title.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Title to a GC_chart — GC_title","text":"","code":"GC_title(   GC_chart,   title = NULL,   subtitle = NULL,   style = list(),   subtitleFont = list(),   titleFont = list(),   show = TRUE,   height = NULL,   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_title.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Title to a GC_chart — GC_title","text":"GC_chart GC chart object. title Character vector. Titles set clusters. subtitle Character vector. Subtitles set clusters. style list CSS styles applied chart container. element list valid CSS property-value pair. example, list(backgroundColor = \"white\", border = \"2px solid black\"). Default empty list. subtitleFont List. Settings subtitle font. titleFont List. Settings title font. show Logical. Whether display title. Default TRUE. height Character. Height title (e.g., \"50px\"). ... Additional customization arguments title subtitle.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_title.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Title to a GC_chart — GC_title","text":"Updated GC chart new title settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_title.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Title to a GC_chart — GC_title","text":"","code":"genes_data <- data.frame(   start = c(10, 50, 90, 130, 170, 210),   end = c(40, 80, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 1, 2, 2, 2) )  # Basic usage GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"400px\") %>% GC_labels(\"name\") %>% GC_title(   title = \"Cluster 1 Data\",   subtitle = \"Detailed View\",   show = TRUE )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"400px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"},\"title\":\"Cluster 1 Data\",\"subtitle\":\"Detailed View\",\"height\":50,\"show\":true},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Customizing title style GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"500px\") %>%   GC_labels(\"name\") %>%   GC_title(     title = \"Cluster 1 Data\",     subtitle = \"Detailed View\",     show = TRUE,     height = \"50px\",     cluster = 1,     x = 0,     y = 25, # height / 2     align = \"center\",     spacing = 20,     style = list(       backgroundColor = \"#0000\"       # Any other CSS styles     ),     titleFont = list(       fontSize = \"16px\",       fontStyle = \"normal\",       fontWeight = \"bold\",       textDecoration = \"normal\",       fontFamily = \"sans-serif\",       cursor = \"default\",       fill = \"black\"       # Any other CSS styles     ),     subtitleFont = list(       fontSize = \"14px\",       fontStyle = \"normal\",       fontWeight = \"bold\",       textDecoration = \"normal\",       fontFamily = \"sans-serif\",       cursor = \"default\",       fill = \"black\"       # Any other CSS styles     )   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"500px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\",\"backgroundColor\":\"#0000\"},\"title\":\"Cluster 1 Data\",\"subtitle\":\"Detailed View\",\"subtitleFont\":{\"fontSize\":\"14px\",\"fontStyle\":\"normal\",\"fontWeight\":\"bold\",\"textDecoration\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"fill\":\"black\"},\"titleFont\":{\"fontSize\":\"16px\",\"fontStyle\":\"normal\",\"fontWeight\":\"bold\",\"textDecoration\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"fill\":\"black\"},\"height\":\"50px\",\"show\":true,\"cluster\":1,\"x\":0,\"y\":25,\"align\":\"center\",\"spacing\":20},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":250,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":250,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_tooltip.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Tooltip for a Gene Chart — GC_tooltip","title":"Set Tooltip for a Gene Chart — GC_tooltip","text":"function configures tooltip gene chart.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_tooltip.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Tooltip for a Gene Chart — GC_tooltip","text":"","code":"GC_tooltip(   GC_chart,   formatter = \"Start:<\/b> {start}
End:<\/b> {end}\",   show = TRUE,   cluster = NULL,   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_tooltip.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Tooltip for a Gene Chart — GC_tooltip","text":"GC_chart gene chart object modified. formatter character string defining HTML content tooltip. can include placeholders like {start} {end} replaced actual data values. default value shows start end data. show Logical, whether display tooltip . cluster Optional; used specify clusters chart tooltips. ... Additional arguments can used customize tooltip.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_tooltip.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Tooltip for a Gene Chart — GC_tooltip","text":"Returns gene chart object tooltip configured.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_tooltip.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set Tooltip for a Gene Chart — GC_tooltip","text":"","code":"# Set tooltip genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5'),   group = c('A', 'B', 'B', 'A', 'C') )  # Add tooltips to the gene chart GC_chart(genes_data, group = \"group\", height = \"200px\") %>% GC_tooltip(formatter = \" Start:<\/b> {start}
end:<\/b> {end}\")  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"cluster\":{\"clusterName\":\"cluster\",\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"cluster\":[\"cluster\",\"cluster\",\"cluster\",\"cluster\",\"cluster\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"formatter\":\" Start:<\\/b> {start}
end:<\\/b> {end}\",\"show\":true}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_trackMouse.html","id":null,"dir":"Reference","previous_headings":"","what":"Track Mouse Movement in a GC_chart — GC_trackMouse","title":"Track Mouse Movement in a GC_chart — GC_trackMouse","text":"function enables disables mouse tracking specified clusters within GC chart. enabled, x y coordinates mouse displayed can used place annotations.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_trackMouse.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Track Mouse Movement in a GC_chart — GC_trackMouse","text":"","code":"GC_trackMouse(GC_chart, show = TRUE, cluster = NULL)"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_trackMouse.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Track Mouse Movement in a GC_chart — GC_trackMouse","text":"GC_chart GC chart object annotations added. show Logical, specifies whether track mouse . cluster Numeric character vector specifying clusters annotations added.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_trackMouse.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Track Mouse Movement in a GC_chart — GC_trackMouse","text":"Updated GC chart object mouse tracking settings.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/reference/GC_trackMouse.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Track Mouse Movement in a GC_chart — GC_trackMouse","text":"","code":"genes_data <- data.frame(   start = c(10, 50, 90, 130, 170, 210),   end = c(40, 80, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 1, 2, 2, 2) )  # Enable mouse tracking GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"220px\") %>% GC_trackMouse()  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"220px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":110,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":true},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":110,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":true},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_transcript.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify Transcript Characteristics within a Chart — GC_transcript","title":"Modify Transcript Characteristics within a Chart — GC_transcript","text":"function updates chart specific characteristics transcripts based given parameters. can show/hide transcripts, apply color scheme, assign custom colors, filter cluster, accept additional options.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_transcript.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify Transcript Characteristics within a Chart — GC_transcript","text":"","code":"GC_transcript(   GC_chart,   transcript = NULL,   type = NULL,   strand = NULL,   group = NULL,   selection = NULL,   show = TRUE,   colorScheme = NULL,   customColors = NULL,   styleExons = list(),   styleIntrons = list(),   styleUTRs = list(),   itemStyleExons = list(),   itemStyleIntrons = list(),   itemStyleUTRs = list(),   labelOptions = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_transcript.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify Transcript Characteristics within a Chart — GC_transcript","text":"GC_chart chart object modified. transcript Optional column name used clustering transcript data. Default NULL. type Column name identifying feature type (\"UTR\", \"exon\"). Default NULL. strand Optional column name indicating strand orientation. Acceptable values include 1, 'forward', 'sense', '+' represent forward strand, -1, 0, 'reverse', 'antisense', \"complement\" '-' represent reverse strand. Default NULL, meaning strand information used. group Optional column name used transcript grouping influence color aesthetics. selection Numeric character, specific transcript filter transcripts . show Logical, whether show transcripts . colorScheme Character NULL, name color scheme use. customColors List NULL, custom colors apply genes. styleExons List, styles apply exons chart. styleIntrons List, styles apply introns chart. styleUTRs List, styles apply UTRs chart. itemStyleExons List, list styles apply individual exons chart. itemStyleIntrons List, list styles apply individual introns chart. itemStyleUTRs List, list styles apply individual UTRs chart. labelOptions List, options styling labels font size, color, position. ... Additional arguments passed gene options.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_transcript.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify Transcript Characteristics within a Chart — GC_transcript","text":"Returns modified gene chart object.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_transcript.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Modify Transcript Characteristics within a Chart — GC_transcript","text":"","code":"transcript_data <- data.frame(   transcript = c(\"transcript1\", \"transcript1\", \"transcript1\", \"transcript1\",                  \"transcript2\", \"transcript2\", \"transcript2\"),   type = c(\"5_utr\", \"exon\", \"exon\", \"3_utr\",            \"5_utr\", \"exon\", \"3_utr\"),   start = c(1, 101, 201, 301,             1, 101, 301),   end = c(50, 150, 250, 350,           50, 150, 350),   strand = rep(\"forward\", 7) )  # All default transcript settings GC_chart(   transcript_data,   start = \"start\",   end = \"end\",   height = \"200px\" ) %>%   GC_transcript(     transcript = \"transcript\",     strand = \"strand\",     type = \"type\",     group = NULL,     show = TRUE,     selection = NULL,     colorScheme = NULL,     customColors = NULL,     styleExons = list(       show = TRUE,       strokeWidth = 0,       cursor = \"default\",       marker = \"box\",       markerSize = \"medium\",       arrowheadWidth = NULL,       arrowheadHeight = NULL,       markerHeight = NULL,       cornerRadius = NULL       # Any other CSS style     ),     styleIntrons = list(       show = TRUE,       strokeWidth = 1,       fill = \"none\",       cursor = \"default\",       marker = \"intron\",       markerSize = \"medium\",       arrowheadWidth = NULL,       arrowheadHeight = NULL,       markerHeight = NULL,       cornerRadius = NULL       # Any other CSS style     ),     styleUTRs = list(       show = TRUE,       fontSize = \"10px\",       fontStyle = \"normal\",       fontFamily = \"sans-serif\",       cursor = \"default\",       color = \"black\",       fill = \"#FFF\",       strokeWidth = 1,       marker = \"box\",       markerSize = \"medium\",       arrowheadWidth = NULL,       arrowheadHeight = NULL,       markerHeight = NULL,       cornerRadius = NULL       # Any other CSS style     ),     labelOptions = list(       show = TRUE,       xOffset = 2,       yOffset = 0,       fontSize = \"12px\",       fontStyle = \"normal\",       fontWeight = \"normal\",       fontFamily = \"sans-serif\",       cursor = \"default\",       color = \"black\"     ),     itemStyleExons = list(),     itemStyleIntrons = list(),     itemStyleUTRs = list()   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"transcript\",\"strand\":\"strand\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"transcript\":[\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\"],\"type\":[\"5_utr\",\"intron\",\"exon\",\"intron\",\"exon\",\"intron\",\"3_utr\",\"5_utr\",\"intron\",\"exon\",\"intron\",\"3_utr\"],\"start\":[1,51,101,151,201,251,301,1,51,101,151,301],\"end\":[50,100,150,200,250,300,350,50,100,150,300,350],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"rowID\":[1,2,3,4,5,6,7,8,9,10,11,12]},\"cluster\":\"transcript\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":null,\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"transcript1\":{\"clusterName\":\"transcript1\",\"data\":{\"transcript\":[\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\"],\"type\":[\"5_utr\",\"intron\",\"exon\",\"intron\",\"exon\",\"intron\",\"3_utr\"],\"start\":[1,51,101,151,201,251,301],\"end\":[50,100,150,200,250,300,350],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"rowID\":[1,2,3,4,5,6,7],\"cluster\":[\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":false},\"sequence\":{\"show\":false},\"scale\":{\"xMin\":1,\"xMax\":350},\"transcript\":{\"show\":true,\"styleExons\":{\"show\":true,\"strokeWidth\":0,\"cursor\":\"default\",\"marker\":\"box\",\"markerSize\":\"medium\",\"arrowheadWidth\":null,\"arrowheadHeight\":null,\"markerHeight\":null,\"cornerRadius\":null},\"styleIntrons\":{\"show\":true,\"strokeWidth\":1,\"fill\":\"none\",\"cursor\":\"default\",\"marker\":\"intron\",\"markerSize\":\"medium\",\"arrowheadWidth\":null,\"arrowheadHeight\":null,\"markerHeight\":null,\"cornerRadius\":null},\"styleUTRs\":{\"show\":true,\"fontSize\":\"10px\",\"fontStyle\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"color\":\"black\",\"fill\":\"#FFF\",\"strokeWidth\":1,\"marker\":\"box\",\"markerSize\":\"medium\",\"arrowheadWidth\":null,\"arrowheadHeight\":null,\"markerHeight\":null,\"cornerRadius\":null},\"labelOptions\":{\"show\":true,\"xOffset\":2,\"yOffset\":0,\"fontSize\":\"12px\",\"fontStyle\":\"normal\",\"fontWeight\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"color\":\"black\"}},\"labels\":{\"group\":null,\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"transcript2\":{\"clusterName\":\"transcript2\",\"data\":{\"transcript\":[\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\"],\"type\":[\"5_utr\",\"intron\",\"exon\",\"intron\",\"3_utr\"],\"start\":[1,51,101,151,301],\"end\":[50,100,150,300,350],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"rowID\":[8,9,10,11,12],\"cluster\":[\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":false},\"sequence\":{\"show\":false},\"scale\":{\"xMin\":1,\"xMax\":350},\"transcript\":{\"show\":true,\"styleExons\":{\"show\":true,\"strokeWidth\":0,\"cursor\":\"default\",\"marker\":\"box\",\"markerSize\":\"medium\",\"arrowheadWidth\":null,\"arrowheadHeight\":null,\"markerHeight\":null,\"cornerRadius\":null},\"styleIntrons\":{\"show\":true,\"strokeWidth\":1,\"fill\":\"none\",\"cursor\":\"default\",\"marker\":\"intron\",\"markerSize\":\"medium\",\"arrowheadWidth\":null,\"arrowheadHeight\":null,\"markerHeight\":null,\"cornerRadius\":null},\"styleUTRs\":{\"show\":true,\"fontSize\":\"10px\",\"fontStyle\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"color\":\"black\",\"fill\":\"#FFF\",\"strokeWidth\":1,\"marker\":\"box\",\"markerSize\":\"medium\",\"arrowheadWidth\":null,\"arrowheadHeight\":null,\"markerHeight\":null,\"cornerRadius\":null},\"labelOptions\":{\"show\":true,\"xOffset\":2,\"yOffset\":0,\"fontSize\":\"12px\",\"fontStyle\":\"normal\",\"fontWeight\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"color\":\"black\"}},\"labels\":{\"group\":null,\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}},\"transcript_called\":true},\"evals\":[],\"jsHooks\":[]}# Change the appearance of a specific intron GC_chart(transcript_data,          start = \"start\",          end = \"end\",          height = \"200px\" ) %>%   GC_transcript(     transcript = \"transcript\",     type = \"type\",     selection = 2,     itemStyleExons = list(list(index = 0, fill = \"red\")     )   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"transcript\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"transcript\":[\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\"],\"type\":[\"5_utr\",\"intron\",\"exon\",\"intron\",\"exon\",\"intron\",\"3_utr\",\"5_utr\",\"intron\",\"exon\",\"intron\",\"3_utr\"],\"start\":[1,51,101,151,201,251,301,1,51,101,151,301],\"end\":[50,100,150,200,250,300,350,50,100,150,300,350],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"rowID\":[1,2,3,4,5,6,7,8,9,10,11,12]},\"cluster\":\"transcript\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":null,\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"transcript1\":{\"clusterName\":\"transcript1\",\"data\":{\"transcript\":[\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\"],\"type\":[\"5_utr\",\"intron\",\"exon\",\"intron\",\"exon\",\"intron\",\"3_utr\"],\"start\":[1,51,101,151,201,251,301],\"end\":[50,100,150,200,250,300,350],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"rowID\":[1,2,3,4,5,6,7],\"cluster\":[\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":false},\"sequence\":{\"show\":false},\"scale\":{\"xMin\":1,\"xMax\":350},\"transcript\":{\"group\":null,\"show\":true},\"labels\":{\"group\":null,\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"transcript2\":{\"clusterName\":\"transcript2\",\"data\":{\"transcript\":[\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\"],\"type\":[\"5_utr\",\"intron\",\"exon\",\"intron\",\"3_utr\"],\"start\":[1,51,101,151,301],\"end\":[50,100,150,300,350],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"rowID\":[8,9,10,11,12],\"cluster\":[\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":false},\"sequence\":{\"show\":false},\"scale\":{\"xMin\":1,\"xMax\":350},\"transcript\":{\"show\":true,\"itemStyleExons\":[{\"index\":0,\"fill\":\"red\"}]},\"labels\":{\"group\":null,\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}},\"transcript_called\":true},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/erythromycin_BlastP.html","id":null,"dir":"Reference","previous_headings":"","what":"Erythromycin BlastP results — erythromycin_BlastP","title":"Erythromycin BlastP results — erythromycin_BlastP","text":"dataset contains detailed information genes involved biosynthesis Erythromycin, antibiotic produced bacterium Saccharopolyspora erythraea several homologous gene clusters identified antiSMASH. includes gene identifiers, chromosomal positions, orientations, annotations regarding products functions, well similarity identity scores BlastP analysis.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/erythromycin_BlastP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Erythromycin BlastP results — erythromycin_BlastP","text":"","code":"erythromycin_BlastP"},{"path":"https://nvelden.github.io/geneviewer/reference/erythromycin_BlastP.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Erythromycin BlastP results — erythromycin_BlastP","text":"data frame 148 observations 16 variables: protein_id Unique protein identifiers. character vector. region chromosomal region gene, indicating start end positions strand. character vector. translation Amino acid sequence protein encoded gene. character vector. cluster Identifier gene cluster gene belongs. character vector. strand strand orientation (\"forward\" \"complement\") gene. character vector. start start position gene chromosome. numeric vector. end end position gene chromosome. numeric vector. rowID unique identifier row dataset. integer vector. identity identity score BlastP analysis, representing percentage identical matches. numeric vector. similarity similarity score BlastP analysis, often reflecting functional structural similarity. numeric vector. BlastP Reference protein_id BlastP comparison, NA applicable. character vector. score Score assigned based BlastP analysis, quantifying match quality. numeric vector. Gene Gene name identifier available, otherwise NA. character vector. Position Formatted string indicating gene's position orientation chromosome. character vector. Product Description gene product. character vector. Functions Functional categorization gene. character vector.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/erythromycin_BlastP.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Erythromycin BlastP results — erythromycin_BlastP","text":"Derived BlastP analysis Saccharopolyspora erythraea genes   involved Erythromycin production.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/erythromycin_cluster.html","id":null,"dir":"Reference","previous_headings":"","what":"Erythromycin Gene Cluster Data — erythromycin_cluster","title":"Erythromycin Gene Cluster Data — erythromycin_cluster","text":"dataset contains information various genes involved biosynthesis Erythromycin, antibiotic produced bacterium Saccharopolyspora erythraea. includes details gene identifiers, start end positions genes, associated functions products.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/erythromycin_cluster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Erythromycin Gene Cluster Data — erythromycin_cluster","text":"","code":"erythromycin_cluster"},{"path":"https://nvelden.github.io/geneviewer/reference/erythromycin_cluster.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Erythromycin Gene Cluster Data — erythromycin_cluster","text":"data frame 23 rows 6 columns: Identifiers Unique identifiers genes. character vector. Start Start positions genes chromosome. numeric vector. End End positions genes chromosome. numeric vector. Strand Strand orientation gene, either \"+\" \"-\". character vector. Product Description gene products. character vector. Functions Functional categorization genes. character vector.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/gbk_features_to_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert GenBank Features to Data Frame — gbk_features_to_df","title":"Convert GenBank Features to Data Frame — gbk_features_to_df","text":"function processes list GenBank features (loaded read_gbk()) converts selected features data frame. supports processing multiple gene clusters.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/gbk_features_to_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert GenBank Features to Data Frame — gbk_features_to_df","text":"","code":"gbk_features_to_df(   gbk_list,   feature = \"CDS\",   keys = NULL,   process_region = TRUE )"},{"path":"https://nvelden.github.io/geneviewer/reference/gbk_features_to_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert GenBank Features to Data Frame — gbk_features_to_df","text":"gbk_list list lists sub-list contains GenBank features specific gene cluster. sub-list expected named list features, feature character vector. feature string specifying feature type extract gene cluster's FEATURE list (e.g., \"CDS\" \"gene\"). Defaults \"CDS\". keys optional vector strings representing specific keys within feature retain final data frame. `NULL` (default), keys within specified feature included. process_region boolean flag; set `TRUE` (default), special processing performed 'region' key (present) extract 'strand', 'start', 'end' information.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/gbk_features_to_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert GenBank Features to Data Frame — gbk_features_to_df","text":"data frame row corresponds feature input   list. data frame includes 'cluster' column indicating source gbk   file.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/gbk_features_to_df.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert GenBank Features to Data Frame — gbk_features_to_df","text":"","code":"if (FALSE) { gbk <- read_gbk(\"path/to/genbank_file.gbk\") df <- gbk_features_to_df(gbk)  # To extract only specific keys within the \"CDS\" feature df <- gbk_features_to_df(gbk, feature = \"CDS\", keys = c(\"gene\", \"region\"))  # To disable special processing of the 'region' key df <- gbk_features_to_df(gbk, process_region = FALSE) }"},{"path":"https://nvelden.github.io/geneviewer/reference/genbank_to_fasta.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert GenBank to FASTA Format — genbank_to_fasta","title":"Convert GenBank to FASTA Format — genbank_to_fasta","text":"function reads GenBank file, extracts sequence writes new file FASTA format. parses DEFINITION VERSION header sequences ORIGIN section.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/genbank_to_fasta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert GenBank to FASTA Format — genbank_to_fasta","text":"","code":"genbank_to_fasta(path, output_dir = NULL)"},{"path":"https://nvelden.github.io/geneviewer/reference/genbank_to_fasta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert GenBank to FASTA Format — genbank_to_fasta","text":"path Path GenBank file. output_dir Optional path output FASTA file. NULL, output saved directory input file base name .fasta extension.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/genbank_to_fasta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert GenBank to FASTA Format — genbank_to_fasta","text":"None explicitly, writes FASTA formatted data file.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/genbank_to_fasta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert GenBank to FASTA Format — genbank_to_fasta","text":"","code":"if (FALSE) { genbank_to_fasta(\"path/to/input.gb\") }"},{"path":"https://nvelden.github.io/geneviewer/reference/geneviewer-shiny.html","id":null,"dir":"Reference","previous_headings":"","what":"Shiny bindings for geneviewer — geneviewer-shiny","title":"Shiny bindings for geneviewer — geneviewer-shiny","text":"Output render functions using geneviewer within Shiny applications interactive Rmd documents.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/geneviewer-shiny.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shiny bindings for geneviewer — geneviewer-shiny","text":"","code":"GC_chartOutput(outputId, width = \"100%\", height = \"400px\")  renderGC_chart(expr, env = parent.frame(), quoted = FALSE)"},{"path":"https://nvelden.github.io/geneviewer/reference/geneviewer-shiny.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shiny bindings for geneviewer — geneviewer-shiny","text":"outputId Output variable read . width, height Must valid CSS unit (like '100 number, coerced string 'px' appended. height Height output widget, must valid CSS unit (like '100 'px' appended. expr expression generates GC chart. env environment evaluate expr. quoted expr quoted expression (quote())? useful want save expression variable.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/geneviewer-shiny.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shiny bindings for geneviewer — geneviewer-shiny","text":"GC_chart widget can placed UI.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/reference/geneviewer-shiny.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Shiny bindings for geneviewer — geneviewer-shiny","text":"","code":"if (interactive()) {   library(shiny)   library(geneviewer)    ui <- fluidPage(     titlePanel(\"Omphalotin Gene Cluster Visualization\"),     mainPanel(       GC_chartOutput(\"gcChart\", width = \"100%\", height = \"500px\")     )   )    server <- function(input, output) {     output$gcChart <- renderGC_chart({       GC_chart(         ophA_clusters, # Ensure 'ophA_clusters' data is defined or available         cluster = \"cluster\",         group = \"class\"       ) %>%       GC_title(title = c(\"O. olearius<\/i>\", \"D. bispora<\/i>\")) %>%       GC_labels(\"name\") %>%       GC_legend(position = \"bottom\") %>%       GC_scaleBar() %>%       GC_clusterLabel(title = \"ophA\")     })   }    shinyApp(ui = ui, server = server) }"},{"path":"https://nvelden.github.io/geneviewer/reference/get_introns.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Intron Positions Based on Exons — get_introns","title":"Calculate Intron Positions Based on Exons — get_introns","text":"function takes dataset containing transcript information calculates start end positions introns based positions exons. generates combined dataframe including original exons calculated introns.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/get_introns.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Intron Positions Based on Exons — get_introns","text":"","code":"get_introns(data)"},{"path":"https://nvelden.github.io/geneviewer/reference/get_introns.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Intron Positions Based on Exons — get_introns","text":"data dataframe containing `start` `end` positions transcripts. Optional columns `type` (exon UTR), `transcript` (containing unique transcript IDs), `strand` (indicating direction, forward reverse, transcript).","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/get_introns.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Intron Positions Based on Exons — get_introns","text":"dataframe original exons calculated introns, sorted   transcript start position. row includes `start`, `end`,   `type` (exon, UTR intron), `transcript`, `strand` segment.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/hs_dystrophin_transcripts.html","id":null,"dir":"Reference","previous_headings":"","what":"Human Dystrophin Transcripts Data — hs_dystrophin_transcripts","title":"Human Dystrophin Transcripts Data — hs_dystrophin_transcripts","text":"dataset contains Exon positions human Dystrophin transcripts 'Dp427p2', 'Dp260-2', 'Dp140', 'Dp116', 'Dp71'.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/hs_dystrophin_transcripts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Human Dystrophin Transcripts Data — hs_dystrophin_transcripts","text":"","code":"hs_dystrophin_transcripts"},{"path":"https://nvelden.github.io/geneviewer/reference/hs_dystrophin_transcripts.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Human Dystrophin Transcripts Data — hs_dystrophin_transcripts","text":"data frame 202 rows 5 columns: transcript Transcript names. character vector representing   names transcripts. type Transcript type. start Start positions. integer vector showing starting   positions Exon. end End positions. integer vector showing ending   positions Exon. length Transcript lengths. integer vector   indicating length transcript.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/human_hox_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Human HOX Gene Cluster Data — human_hox_genes","title":"Human HOX Gene Cluster Data — human_hox_genes","text":"dataset represents positions clusters various human HOX genes. HOX genes group related genes control body plan embryo along head-tail axis. dataset includes genes HOXA, HOXB, HOXC, HOXD clusters.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/human_hox_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Human HOX Gene Cluster Data — human_hox_genes","text":"","code":"human_hox_genes"},{"path":"https://nvelden.github.io/geneviewer/reference/human_hox_genes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Human HOX Gene Cluster Data — human_hox_genes","text":"data frame 39 rows 6 columns: symbol HGNC symbols HOX genes. character vector. chromosome_name Chromosome number gene located. numeric vector. start Start positions genes chromosome. numeric vector. end End positions genes chromosome. numeric vector. strand -1 reverse 1 forward. cluster Cluster identification character vector,   specifying HOX gene cluster (HOXA, HOXB, HOXC, HOXD). name Simplified names HOX genes. character vector.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/mummer_alignment.html","id":null,"dir":"Reference","previous_headings":"","what":"Perform Sequence Alignment Using MUMmer — mummer_alignment","title":"Perform Sequence Alignment Using MUMmer — mummer_alignment","text":"function orchestrates alignment sequences specified directory using MUMmer, tool aligning large DNA protein sequences. can handle GenBank FASTA file formats. performs checks ensure necessary files present.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/mummer_alignment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Perform Sequence Alignment Using MUMmer — mummer_alignment","text":"","code":"mummer_alignment(   path,   cluster = NULL,   maptype = \"many-to-many\",   seqtype = \"protein\",   mummer_options = \"\",   filter_options = \"\",   remove_files = TRUE,   output_dir = NULL )"},{"path":"https://nvelden.github.io/geneviewer/reference/mummer_alignment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Perform Sequence Alignment Using MUMmer — mummer_alignment","text":"path directory containing sequence files. cluster Optional vector cluster names consider alignment. NULL, clusters inferred file names. order names determines alignment sequence. maptype type mapping perform; \"many--many\" \"one--one\". \"many--many\" allows multiple matches clusters, \"one--one\" restricts alignments unique matches pair. seqtype type sequences, either \"protein\" \"nucleotide\". mummer_options Additional command line options MUMmer. see available options, can run `nucmer --help` `promer --help` terminal depending whether aligning nucleotide protein sequences. filter_options Additional options filtering MUMmer results. view filtering options, run `delta-filter --help` terminal. remove_files Logical indicating whether remove intermediate files generated process, defaults TRUE. output_dir Optional directory save output files; defaults NULL, uses input file directory outputs.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/mummer_alignment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Perform Sequence Alignment Using MUMmer — mummer_alignment","text":"data frame combining alignment results, NULL errors occur   processing.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/mummer_alignment.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Perform Sequence Alignment Using MUMmer — mummer_alignment","text":"Kurtz S, Phillippy , Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL (2004). Versatile open software comparing large genomes. Genome Biology, 5(R12).","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/mummer_alignment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Perform Sequence Alignment Using MUMmer — mummer_alignment","text":"","code":"if (FALSE) { # Basic alignment with default options mummer_alignment(   path = \"/path/to/sequences\",   maptype = \"many-to-many\",   seqtype = \"protein\" ) # Alignment with specific MUMmer options mummer_alignment(   path = \"/path/to/sequences\", maptype = \"one-to-one\", seqtype = \"protein\",   mummer_options = \"--maxgap=500 --mincluster=100\",   filter_options = \"-i 90\"   )  }"},{"path":"https://nvelden.github.io/geneviewer/reference/ophA_clusters.html","id":null,"dir":"Reference","previous_headings":"","what":"ophA Gene Cluster from Omphalotus olearius — ophA_clusters","title":"ophA Gene Cluster from Omphalotus olearius — ophA_clusters","text":"dataset represents ophA gene cluster Omphalotus olearius Dendrothele bispora, involved production omphalotin, cyclic N-methylated peptide.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/ophA_clusters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ophA Gene Cluster from Omphalotus olearius — ophA_clusters","text":"","code":"ophA_clusters"},{"path":"https://nvelden.github.io/geneviewer/reference/ophA_clusters.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"ophA Gene Cluster from Omphalotus olearius — ophA_clusters","text":"data frame 17 rows 5 columns: name Gene names. character vector. start Start positions genes. integer vector. end End positions genes. integer vector. class Classifications genes. character vector indicating   type protein function associated gene. cluster Cluster identification character vector, specifying whether   gene belongs ophA dbophA gene cluster.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/ophA_clusters.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"ophA Gene Cluster from Omphalotus olearius — ophA_clusters","text":"van der Velden NS et al. Autocatalytic backbone N-methylation family ribosomal peptide natural products. Nat Chem Biol. 2017 Aug;13(8):833-835. doi: 10.1038/nchembio.2393. Epub 2017 Jun 5. PMID: 28581484.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/protein_blast.html","id":null,"dir":"Reference","previous_headings":"","what":"Perform Protein BLAST Analysis Within Specified Clusters — protein_blast","title":"Perform Protein BLAST Analysis Within Specified Clusters — protein_blast","text":"function conducts BLAST analysis protein sequences within specified clusters. generates possible protein combinations query cluster clusters, performs pairwise alignments, calculates sequence identity similarity, filters results based minimum identity threshold.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/protein_blast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Perform Protein BLAST Analysis Within Specified Clusters — protein_blast","text":"","code":"protein_blast(   data,   query,   id = \"protein_id\",   start = \"start\",   end = \"end\",   cluster = \"cluster\",   genes = NULL,   identity = 30,   parallel = TRUE )"},{"path":"https://nvelden.github.io/geneviewer/reference/protein_blast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Perform Protein BLAST Analysis Within Specified Clusters — protein_blast","text":"data dataframe character vector specifying path .gbk files. character vector provided, interpreted file paths .gbk files read processed. dataframe must contain columns unique protein identifiers, cluster identifiers, protein sequences, start end positions gene. query name query cluster used BLAST comparisons. id name column contains gene identifiers. Defaults \"protein_id\". start name column specifying start positions genes. Defaults \"start\". end name column specifying end positions genes. Defaults \"end\". cluster name column specifying cluster names. Defaults \"cluster\". genes optional vector gene identifiers include analysis. Defaults NULL. identity Minimum identity threshold BLAST hits considered significant. Defaults 30. parallel Logical indicating whether use parallel processing alignments. Defaults TRUE.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/protein_blast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Perform Protein BLAST Analysis Within Specified Clusters — protein_blast","text":"modified version input `data` dataframe, including   additional columns BLAST results (identity, similarity).","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/protein_blast.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Perform Protein BLAST Analysis Within Specified Clusters — protein_blast","text":"function relies Biostrings pwalign package sequence alignment dplyr package data manipulation. Ensure packages installed loaded R session.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/protein_blast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Perform Protein BLAST Analysis Within Specified Clusters — protein_blast","text":"","code":"if (FALSE) { path_to_folder <- \"path/to/gbk/folder/\" data_updated <- protein_blast(                          path_to_folder,                          id = \"protein_id\",                          query = \"cluster A\",                          identity = 30                          ) }"},{"path":"https://nvelden.github.io/geneviewer/reference/read_bed.html","id":null,"dir":"Reference","previous_headings":"","what":"Read BED Files — read_bed","title":"Read BED Files — read_bed","text":"function reads BED files specified directory file path combines single data frame. BED files use 0-based coordinate starts, function transforms coordinates 1-based import.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_bed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read BED Files — read_bed","text":"","code":"read_bed(path)"},{"path":"https://nvelden.github.io/geneviewer/reference/read_bed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read BED Files — read_bed","text":"path character string specifying directory containing BED files file path single BED file.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_bed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read BED Files — read_bed","text":"data frame combining data BED files.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_bed.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read BED Files — read_bed","text":"function can read multiple BED files directory   single BED file specified path. adds 'filename' column   name file, combines data frames files one.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_bed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read BED Files — read_bed","text":"","code":"if (FALSE) { # Read BED files from a directory bed_data <- read_bed(\"path/to/directory\")  # Read a single BED file bed_data <- read_bed(\"path/to/file.bed\") }"},{"path":"https://nvelden.github.io/geneviewer/reference/read_fasta.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Protein Sequences from FASTA Files — read_fasta","title":"Read Protein Sequences from FASTA Files — read_fasta","text":"function reads protein sequences specified FASTA file FASTA files within directory. specifically looks metadata FASTA headers key-value pairs separated equals sign `=`. example, header '>protein1 [gene=scnD] [protein=ScnD]', extracts 'gene' key 'scnD' value, similarly key-value pairs.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_fasta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Protein Sequences from FASTA Files — read_fasta","text":"","code":"read_fasta(fasta_path, sequence = TRUE, keys = NULL, file_extension = \"fasta\")"},{"path":"https://nvelden.github.io/geneviewer/reference/read_fasta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Protein Sequences from FASTA Files — read_fasta","text":"fasta_path Path FASTA file directory containing FASTA files. sequence Logical; `TRUE`, protein sequences included returned data frame. keys optional vector strings representing specific keys within fasta header retain final data frame. `NULL` (default), keys within specified feature included. file_extension Extension FASTA files read directory (default 'fasta').","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_fasta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Protein Sequences from FASTA Files — read_fasta","text":"data frame columns piece information extracted  FASTA headers.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_fasta.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read Protein Sequences from FASTA Files — read_fasta","text":"Biostrings package required run function.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_fasta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Protein Sequences from FASTA Files — read_fasta","text":"","code":"if (FALSE) { # Read sequences from a single FASTA file sequences_df <- read_fasta(\"path/to/single_file.fasta\")  # Read all sequences from a directory of FASTA files sequences_df <- read_fasta(\"path/to/directory/\", file_extension = \"fa\")  # Read sequences and include the protein sequences in the output sequences_df <- read_fasta(\"path/to/directory/\", sequence = TRUE) }"},{"path":"https://nvelden.github.io/geneviewer/reference/read_gbk.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Data from GenBank Files — read_gbk","title":"Read Data from GenBank Files — read_gbk","text":"function reads data single GenBank file directorty GenBank files. allows selective extraction information specifying sections features.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_gbk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Data from GenBank Files — read_gbk","text":"","code":"read_gbk(path, sections = NULL, features = NULL, origin = TRUE)"},{"path":"https://nvelden.github.io/geneviewer/reference/read_gbk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Data from GenBank Files — read_gbk","text":"path string representing file path target GenBank (.gbk) file directory. sections optional vector strings representing names specific sections within GenBank file extract (e.g., \"LOCUS\", \"DEFINITION\", \"ACCESSION\", \"VERSION\"). `NULL` (default), function extracts available sections. features optional vector strings indicating specific feature types extract FEATURES section GenBank file (e.g., \"CDS\", \"gene\", \"mRNA\"). `NULL` (default), function extracts feature types present FEATURES section. origin boolean flag; set `TRUE` (default), origin sequence data included output.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_gbk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Data from GenBank Files — read_gbk","text":"list containing contents specified sections features   GenBank file. section feature returned separate   list element.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_gbk.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Data from GenBank Files — read_gbk","text":"","code":"if (FALSE) { # Read all data from a GenBank file gbk_data <- read_gbk(\"path/to/genbank_file.gbk\")  # Read all data from a directory of GenBank files gbk_data <- read_gbk(\"path/to/genbank/directory\")  # Read only specific sections from a GenBank file gbk_data <- read_gbk(   \"path/to/genbank_file.gbk\",   sections = c(\"LOCUS\", \"DEFINITION\") )  # Read specific features from the FEATURES section of a GenBank file gbk_data <- read_gbk(\"path/to/genbank_file.gbk\", features = c(\"gene\", \"CDS\"))  # Read data without the origin sequence gbk_data <- read_gbk(\"path/to/genbank_file.gbk\", origin = FALSE) }"},{"path":"https://nvelden.github.io/geneviewer/reference/read_gff.html","id":null,"dir":"Reference","previous_headings":"","what":"Read GFF Files — read_gff","title":"Read GFF Files — read_gff","text":"function reads GFF files specified directory file path combines single data frame.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_gff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read GFF Files — read_gff","text":"","code":"read_gff(path, fields = NULL)"},{"path":"https://nvelden.github.io/geneviewer/reference/read_gff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read GFF Files — read_gff","text":"path character string specifying directory containing GFF files file path single GFF file. fields optional vector character strings specifying fields extract GFF files.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_gff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read GFF Files — read_gff","text":"data frame containing combined data GFF files.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_gff.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read GFF Files — read_gff","text":"function can read multiple GFF files directory   single GFF file. processes file, extracts specified fields (  provided), adds 'name' column filename, combines data   frames files one.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_gff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read GFF Files — read_gff","text":"","code":"if (FALSE) { # Read GFF files from a directory gff_data <- read_gff(\"path/to/directory\")  # Read a single GFF file gff_data <- read_gff(\"path/to/file.gff\")  # Read specific fields from GFF files gff_data <- read_gff( \"path/to/directory\", fields = c(\"seqid\", \"start\", \"end\", \"attributes\") ) }"},{"path":"https://nvelden.github.io/geneviewer/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. magrittr %>%","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-8","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.8","text":"Option display transcripts using GC_transcripts function.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-7","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.7","text":"Option perform MUMmer alignments. Add option add color bar.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-6","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.6","text":"Option perfrom BlastP gene clusters. Add option add links genes clusters.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-5","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.5","text":"Add preset markers genes: arrow, boxarrow, box, cbox rbox. Add options load cluster information GenBank FASTA files.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-4","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.4","text":"Add option add gene links. Change package name GCVieweR geneviewer.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-3","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.3","text":"Option align specified gene across clusters.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-2","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.2","text":"Options add text, line, arrow, rectangle, symbol, terminator promoter annotations GC_chart.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-1","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.1","text":"Introduced customizable margin settings charts, clusters, titles, legends. Added styling options containers charts, clusters, titles, legends. Implemented new feature display clusters side side. Updated expanded documentation reflect new features usability improvements.","code":""},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"geneviewer-010","dir":"Changelog","previous_headings":"","what":"geneviewer 0.1.0","title":"geneviewer 0.1.0","text":"Initial Beta release.","code":""}]
+[{"path":"https://nvelden.github.io/geneviewer/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2023 geneviewer authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/BLASTP.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Cluster comparison using BlastP","text":"tutorial describes can use geneviewer identify visualize homologous genes across clusters performing BlastP alignment. demonstrate use GenBank file contains genes involved biosynthesis erythromycin Saccharopolyspora erythraea compare several homologous clusters different species identified using antiSMASH. guidance importing clusters GenBank files, please refer guide.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/BLASTP.html","id":"materials","dir":"Articles","previous_headings":"","what":"Materials","title":"Cluster comparison using BlastP","text":".gbk files additional gene info can downloaded geneviewer-tutorials repository. visualization, geneviewer package required. Sequence alignment performed using Biostrings pwalign packages can downloaded Bioconductor. Optionally, parallel package can utilized increase processing times.","code":"devtools::install_github(\"nvelden/geneviewer\") BiocManager::install(\"Biostrings\") BiocManager::install(\"pwalign\") # Optional but recommended for speeding up processing install.packages(\"parallel\")   library(geneviewer) library(Biostrings) library(pwalign) library(parallel)"},{"path":"https://nvelden.github.io/geneviewer/articles/BLASTP.html","id":"loading-cluster-information","dir":"Articles","previous_headings":"","what":"Loading cluster information","title":"Cluster comparison using BlastP","text":"cluster information needed run BlastP can loaded directly .gbk files pointing folder path contains files running protein_blast() function. Alternatively, protein blast can performed using data.frame contains start, end, strand, translation well unique identifier gene cluster shown .","code":"# change the path to the folder where the .gbk files are saved folder_path <- \"~/path/to/folder/\""},{"path":"https://nvelden.github.io/geneviewer/articles/BLASTP.html","id":"run-blastp","dir":"Articles","previous_headings":"","what":"Run BlastP","title":"Cluster comparison using BlastP","text":"tutorial, directly input folder path protein_blast() function load data. ’ll select BGC0000055 query cluster conduct BlastP analysis find homologous clusters. use 30 minimum identity threshold. Performing BlastP analysis dataset can take several minutes set parallel processing TRUE. smaller datasets parallel package installed, set parallel processing FALSE. running BlastP, dataset contain three additional columns. colums : BlastP: Indicates top BlastP match found within query cluster, characterized unique protein id. identity: percentage identity BlastP hit. similarity: percentage similarity BlastP hit. score: Synteny score clusters based used antiSMASH/MultiGeneBlast. can visualize results using geneviewer. graph clusters ordered based synteny score. genes colored BlasP hit found query cluster. Genes remain uncolored significant homologous. hoovering genes one can see percentage identity similarity.","code":"BlastP_results <- geneviewer::protein_blast(   folder_path,   query = \"BGC0000055\",   id = \"protein_id\", # Name of column containing gene identifiers.    cluster = \"cluster\", # Name of column containing cluster identifiers.    identity = 30,   parallel = TRUE ) GC_chart(   data = BlastP_results,   cluster = \"cluster\",   strand = \"strand\",   group = \"BlastP\",   height = \"400px\" ) %>% GC_clusterLabel() %>% GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/BLASTP.html","id":"color-by-gene-function","dir":"Articles","previous_headings":"","what":"Color by gene function","title":"Cluster comparison using BlastP","text":"Rather assigning colors genes based BlastP matches, can color gene function. can bind extra gene information specific query cluster BGC0000055_info.csv file. executing left_join() operation BlastP_results dataset BlastP field, can add extra information BlastP results. can now use Function category color genes. ’ll also add gene names, links, BlastP identity values cluster information. Alternatively, GC_links() function allows highlighting connections specific genes utilizing value1 value2 parameters. gain insights cluster sizes, can adjust axis_type range. additional styling coloring options, refer GC_links() GC_scale documentation.","code":"# change the path to the folder where the .gbk files are saved BGC0000055_info <- \"~/path/to/folder/BGC0000055_info.csv\" BlastP_results_functions <- left_join(BlastP_results, BGC0000055_info, by = dplyr::join_by(BlastP == protein_id ) ) GC_chart(   data = BlastP_results_functions,   cluster = \"cluster\",   group = \"Functions\",   strand = \"strand\",   height = \"600px\" ) %>% GC_labels(label = \"Gene\", cluster = 1) %>%  GC_links(group = \"BlastP\",  measure = \"identity\") %>%   GC_clusterLabel() %>% GC_legend(TRUE) GC_chart(   data = BlastP_results_functions,   cluster = \"cluster\",   group = \"Functions\",   strand = \"strand\",   height = \"600px\" ) %>% GC_labels(label = \"Gene\", cluster = 1) %>%  GC_scale(axis_type = \"range\") %>% GC_links(group = \"Gene\",            value1 = c(\"eryAI\", \"eryAII\", \"eryAIII\"),           value2 = c(\"eryAI\", \"eryAII\", \"eryAIII\"),           use_group_colors = TRUE          ) %>%   GC_clusterLabel() %>% GC_legend(TRUE)"},{"path":"https://nvelden.github.io/geneviewer/articles/Examples.html","id":"e-coli-lac-operon","dir":"Articles","previous_headings":"","what":"E.coli Lac operon","title":"Example charts","text":"","code":"lacZ_operon <- data.frame(   start = c(361249, 361926, 363231, 366428),    end = c(361860, 363179, 366305, 367510),    Gene_symbol = c(\"lacA\", \"lacY\", \"lacZ\", \"lacI\"),    Strand = c(\"minus\", \"minus\", \"minus\", \"minus\"),    NCBI_Gene_ID = as.character(c(945674, 949083, 945006, 945007)),    Description = c(\"galactoside O-acetyltransferase\",                    \"lactose permease\", \"beta-galactosidase\",                    \"DNA-binding transcriptional repressor LacI\") )  GC_chart(lacZ_operon, group = \"Gene_symbol\", height = \"140px\") %>%   GC_labels() %>%   GC_scaleBar(title = \"0.2 kb\", scaleBarUnit = 200, y=30) %>%   GC_tooltip(     formatter = \"     ID:<\/b> {NCBI_Gene_ID}
     Description:<\/b> {Description}
     Start:<\/b> {start}
     End:<\/b> {end}\",   ) %>%   GC_clusterFooter(     align = \"center\",     y = -30,     subtitle = \"Escherichia coli<\/i> str. K-12 substr. MG1655\"    ) %>%   GC_coordinates(     rotate = 0,     tickValuesBottom = c(min(lacZ_operon$start), max(lacZ_operon$end)),     textStyle = list(fontSize = \"10px\", x = -2.2, y = 1.2),     tickStyle = list(lineLength = 10)     ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/Examples.html","id":"omphalotin-gene-clusters","dir":"Articles","previous_headings":"","what":"Omphalotin gene clusters","title":"Example charts","text":"","code":"GC_chart(ophA_clusters,             start = \"start\",            end = \"end\",            group = \"class\",            cluster = \"cluster\") %>%   GC_clusterFooter(     title = c(\"Omphalotus olearius<\/i>\", \"Dendrothele bispora<\/i>\"),      subtitle = c(\"Locus: 2,522 - 21,484\", \"Locus: 19,236 - 43,005\"),     align = \"left\",     x = 50) %>%   GC_legend(position = \"top\") %>%   GC_labels(label = \"name\") %>%   GC_scaleBar(y = 20) %>%   GC_scale(cluster = 1,  scale_breaks = TRUE, hidden = TRUE) %>%   GC_scale(cluster = 2, reverse = TRUE, hidden = TRUE) %>%   GC_tooltip(     formatter = \"Gene:<\/b> {name}
 Start:<\/b> {start}
end:<\/b> {end}\"   )"},{"path":"https://nvelden.github.io/geneviewer/articles/Examples.html","id":"h--sapiens-hox-genes-using-biomart","dir":"Articles","previous_headings":"","what":"H. sapiens Hox genes using biomaRt","title":"Example charts","text":"","code":"# Get HOX gene positions  library(biomaRt)  ensembl <- useMart(\"ensembl\", dataset = \"hsapiens_gene_ensembl\")  hox_gene_sets <- list(   HOXA = c(\"HOXA1\", \"HOXA2\", \"HOXA3\", \"HOXA4\", \"HOXA5\", \"HOXA6\", \"HOXA7\", \"HOXA9\", \"HOXA10\", \"HOXA11\", \"HOXA13\"),   HOXB = c(\"HOXB1\", \"HOXB2\", \"HOXB3\", \"HOXB4\", \"HOXB5\", \"HOXB6\", \"HOXB7\", \"HOXB8\", \"HOXB9\", \"HOXB13\"),   HOXC = c(\"HOXC4\", \"HOXC5\", \"HOXC6\", \"HOXC8\", \"HOXC9\", \"HOXC10\", \"HOXC11\", \"HOXC12\", \"HOXC13\"),   HOXD = c(\"HOXD1\", \"HOXD3\", \"HOXD4\", \"HOXD8\", \"HOXD9\", \"HOXD10\", \"HOXD11\", \"HOXD12\", \"HOXD13\") )  get_gene_positions <- function(gene_list, cluster_name) {    result <- getBM(attributes = c('hgnc_symbol', 'chromosome_name', 'strand', 'start_position', 'end_position'),                   filters = 'hgnc_symbol',                   values = gene_list,                   mart = ensembl)   transform(result, cluster = cluster_name) }  # Apply get_gene_positions to each gene set hox_gene_positions <- base::lapply(names(hox_gene_sets), function(cluster_name) {   get_gene_positions(hox_gene_sets[[cluster_name]], cluster_name) })  # Combine the results into a single data frame combined_hox_genes <- do.call(rbind, hox_gene_positions)  # Add gene names combined_hox_genes$name <- paste0(substr(combined_hox_genes$hgnc_symbol, 1, 3), substr(combined_hox_genes$hgnc_symbol, 5, nchar(combined_hox_genes$hgnc_symbol))) GC_chart(   combined_hox_genes,   start = \"start_position\",   end = \"end_position\",   group = \"cluster\",   height = \"400px\",   strand = \"strand\",   cluster = \"cluster\") %>%   GC_sequence(y=45) %>%   GC_legend(FALSE) %>%   GC_clusterLabel(title = unique(human_hox_genes$cluster)) %>%   GC_genes(     marker = \"boxarrow\",     markerHeight = 10,     arrowheadHeight = 10,     arrowheadWidth = 3   ) %>%    GC_labels(label = \"name\", fontSize = \"10px\", adjustLabels = FALSE) %>%   GC_labels(cluster = 2, label = \"name\", itemStyle = list(list(index = 5, x = -4))) %>%   GC_scale(     cluster = c(1,2),     hidden = TRUE,     reverse = TRUE   ) %>%   GC_cluster(prevent_gene_overlap = TRUE, overlap_spacing=20)"},{"path":"https://nvelden.github.io/geneviewer/articles/Examples.html","id":"brca1-splice-variants","dir":"Articles","previous_headings":"","what":"BRCA1 splice variants","title":"Example charts","text":"","code":"GC_chart(BRCA1_splice_variants, height = \"600px\") %>%   GC_transcript(     transcript = \"ensembl_transcript_id\",      strand = \"strand\",      type = \"type\",   ) %>%   GC_clusterTitle(     title = unique(BRCA1_splice_variants$ensembl_transcript_id),     titleFont = list(       fontSize = \"12px\"     )   ) %>%   GC_clusterFooter(     title = c(\"0.8%\", \"0.1%\", \"0.07%\", \"0.02%\", \"0.01%\"),     align = \"center\"   )"},{"path":"https://nvelden.github.io/geneviewer/articles/Examples.html","id":"saccharopolyspora-erythraea-erythromycin","dir":"Articles","previous_headings":"","what":"Saccharopolyspora erythraea Erythromycin","title":"Example charts","text":"","code":"colors <- list(   \"Tailoring (Hydroxylation)\" = \"#d62728\",    \"Precursor biosynthesis\" = \"#2ca02c\",   \"Tailoring (Glycosylation)\" = \"#e6b0aa\",    \"Scaffold biosynthesis\" = \"#9467bd\",    \"Tailoring (Methylation)\" = \"#8b0000\",    \"Activation / processing\" = \"#1f77b4\",    \"Resistance / immunity\" = \"#f7dc6f\" ,   \"Other\" = \"#808080\" )  GC_chart(erythromycin_cluster,           start = \"Start\",          end = \"End\",          height = \"160px\",          group = \"Functions\") %>%   GC_title(     title = \"Erythromycin A biosynthetic gene cluster from Saccharopolyspora erythraea<\/i>\",     height = 40,     align = \"left\"     ) %>%   GC_genes(     marker = \"boxarrow\",     marker_size = \"small\"   ) %>%   GC_tooltip(     formatter = \"{Identifiers}<\/b>                  
{Product}                  
{start} - {end}({Strand})\"    ) %>%   GC_scale(     start = 778000,     end = 832000,     ticksCount = 8   ) %>%   GC_legend(     legendTextOptions = list(fontSize = \"12px\"),     order = c(setdiff(sort(erythromycin_cluster$Functions), \"Other\"), \"Other\")          ) %>%   GC_color(customColors = colors)"},{"path":"https://nvelden.github.io/geneviewer/articles/Examples.html","id":"saccharopolyspora-erythraea-erythromycin-blastp","dir":"Articles","previous_headings":"","what":"Saccharopolyspora erythraea Erythromycin BlastP","title":"Example charts","text":"","code":"### Erythromycin BlastP GC_chart(erythromycin_BlastP,           cluster = \"cluster\",          strand = \"strand\",          group = \"Functions\",          height = 700) %>%   GC_title(     title = \"BlastP Results\"   ) %>%   GC_labels(\"Gene\", cluster = 1) %>%   GC_links(group = \"Gene\",             show_links = FALSE,            color_bar = FALSE,            labelStyle = list(fontSize = \"10px\")            ) %>%   GC_clusterLabel() library(dplyr) ### Erythromycin BlastP GC_chart(erythromycin_BlastP %>% dplyr::filter(cluster %in% c(\"BGC0000055\", \"BGC0000054\")),           cluster = \"cluster\",          strand = \"strand\",          group = \"BlastP\",          height = 250) %>%   GC_labels(\"Gene\", cluster = 1) %>%   GC_genes(marker_size = \"small\", marker = \"rbox\", markerHeight = 15) %>%   GC_links(group = \"BlastP\",             label = FALSE,            color_bar = FALSE            ) %>%   GC_clusterLabel() %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadFastaFiles.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Loading Gene Clusters From FASTA Files","text":"tutorial demonstrates creating gene cluster visualizations FASTA files using geneviewer. guidance importing clusters GenBank files see: link. geneviewer parses FASTA headers extract key-value pairs, denoted =. instance, FASTA header identifies ‘protein’ ‘putative phosphoenolpyruvate synthase’ similarly processes pairs. ‘location’ tag crucial allows extraction ‘start’, ‘end’, ‘strand’ information gene.","code":">lcl|HQ3864.1_prot_ADX475.1_1 protein=putative phosphoenolpyruvate synthase protein_id=ADX66475.1 location=complement(<1..2247) gbkey=CDS MRATGLVRGRAAKRFGRAGGAGDAIGQCRATGHDCLGGSAMIEQYVWDLHEVDETQVAVVGGKGAHLGGL SRIEGIRVPAGFCVTTDAFRRIMAEAPSIDDGLDQLSRLNPDDREAIRTLSAQIRRTIEGIAIPGDLAAA ITRALARLGEHAACAVRSSATAEDLPTASFAGQQDTYLNVVGPTAILQHVSRCWASLFTERAVTYRQRNG"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadFastaFiles.html","id":"materials","dir":"Articles","previous_headings":"","what":"Materials","title":"Loading Gene Clusters From FASTA Files","text":"FASTA files uses tutorial originally downloaded NCBI website can downloaded directly geneviewer-tutorials repository.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/LoadFastaFiles.html","id":"loading-fasta-files","dir":"Articles","previous_headings":"","what":"Loading FASTA files","title":"Loading Gene Clusters From FASTA Files","text":"example FASTA files used tutorial different organism holds genes cluster produces polyene antifungal agent. Download files place folder. can read files R using read_fasta function geneviewer. function uses Biostrings library need load well. function parse FASTA headers create data.frame extracted information. set sequence FALSE since need sequences create cluster visualization. data.frame holds protein IDs, start, end strand information gene. addition cluster column tells us file gene coming.","code":"library(geneviewer) # if (!require(\"BiocManager\", quietly = TRUE)) #     install.packages(\"BiocManager\") #  # BiocManager::install(\"Biostrings\") library(Biostrings)  # change the path to the folder where you have saved the file file_path <- \"~/path/to/folder/\" fasta_df <- read_fasta(file_path, sequence = FALSE) View(fasta_df) # Inspect the data.frame in Rstudio"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadFastaFiles.html","id":"cluster-visualization","dir":"Articles","previous_headings":"","what":"Cluster Visualization","title":"Loading Gene Clusters From FASTA Files","text":"Using data.frame created FASTA files can now easily make cluster visualization.","code":"# Make the cluster chart chart <- GC_chart(   fasta_df,   start = \"start\",   end = \"end\",   strand = \"strand\",   cluster = \"cluster\",   height = \"400px\" ) %>%    GC_clusterLabel(unique(fasta_df$cluster)) chart"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadFastaFiles.html","id":"uniprot-keywords","dir":"Articles","previous_headings":"","what":"Uniprot Keywords","title":"Loading Gene Clusters From FASTA Files","text":"can get additional information gene using Uniprot.ws package. make connection database using UniProt.ws function. Using keytypes() can see keys can use query database columns() can see different fields can get return. gene IDs EMBL-GenBank-DDBJ_CDS identifiers. tutorial want return keywords associated gene can use group genes based function. return data.frame original identifiers, uniprotIDs keywords associated gene. now bit data wrangling help dplyr package performing following steps: split keywords gene “;” Count occurrence keyword gene keep highest occurring keyword Replace keyword less 10 occurrences “” Bind keywords fasta_df protein ID Replace genes without keyword Select columns need visualization can now make visual use keywords group genes. alter order legend alphabetical order group placed last finally customize tooltip also show protein Id hoover. customization options like setting title, altering colors adding gene links much see Get Started Examples.","code":"library(UniProt.ws)  up <- UniProt.ws::UniProt.ws()  keytypes(up) columns(up)  keywords <- UniProt.ws::select(   up,    column = c(\"keyword\"),    keys = fasta_df$protein_id,    keytype = \"EMBL-GenBank-DDBJ_CDS\"   ) library(dplyr)  keywords_count <- keywords %>%   # Separate the Keywords into different rows   tidyr::separate_rows(Keywords, sep = \";\") %>%   # Replace NA values with 'Other'   mutate(Keywords = replace(Keywords, is.na(Keywords), \"Other\")) %>%   # Add a Count column that counts each Keyword   add_count(Keywords)  # Keep top ranking keywords for each protein ID keywords_count <- keywords_count %>%   group_by(From) %>%   filter(rank(-n, ties.method = \"first\") == 1) %>%   ungroup()  # Replace any keyword that has a count less then 10 with \"Other\" keywords_count <- keywords_count %>%   mutate(Keywords = ifelse(n < 10, \"Other\", Keywords))  # Bind Keywords back to fasta_df fasta_df_with_keywords <-    left_join(fasta_df, keywords_count, by = c(\"protein_id\" = \"From\")) %>%    mutate(Keywords = replace(Keywords, is.na(Keywords), \"Other\")) %>%   select(cluster, start, end, strand, protein_id, protein, Keywords, n) key_legend <- c(setdiff(sort(unique(fasta_df_with_keywords$Keywords)), \"Other\"), \"Other\")  # Make the cluster chart chart <- GC_chart(   fasta_df_with_keywords,   start = \"start\",   end = \"end\",   strand = \"strand\",   group = \"Keywords\",   cluster = \"cluster\",   height = \"400px\" ) %>%    GC_clusterLabel(unique(fasta_df$cluster)) %>%   GC_legend(order = key_legend) %>%   GC_tooltip(     formatter = \"     ProteinID:<\/b> {protein_id}
     Region:<\/b> {start} - {end}     \"   ) chart"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGFF.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Loading Gene Clusters From Generic Feature Format (GFF) Files","text":"tutorial demonstrates creating gene cluster visualizations Generic Feature Format (GFF) files using geneviewer. can obtain .gff files variety platforms NCBI, Ensembl UCSC. tutorial demonstrates load visualize several viral genomes .gff format using geneviewer.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGFF.html","id":"materials","dir":"Articles","previous_headings":"","what":"Materials","title":"Loading Gene Clusters From Generic Feature Format (GFF) Files","text":".gff files retrieved Ensembl website searching respective GenBank identifiers downloading records GFF3 format. Alternatively, files can also directly accessed geneviewer-tutorials repository.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGFF.html","id":"loading-gff-files","dir":"Articles","previous_headings":"","what":"Loading GFF files","title":"Loading Gene Clusters From Generic Feature Format (GFF) Files","text":"can load .gff files R using read_gff function geneviewer package. , can either load file individually specifying file path, load files specifying directory contains .gff files. example , load .gff files specified directory using fields parameter select specific fields loading. fields specified, fields loaded default. Using dplyr package, filter data select entries ‘type’ column contains ‘CDS’. addition add extra column maps GenBank ID filename column corresponding viral name. can now visualize genomic data using geneviewer. chart displays start end positions genes viral genome oriented according strand location. custom title added chart, gene clusters labeled viral names. axis set range facilitate size comparisons among genomes. Additionally, visual representation genes simplified removing outlines (strokes) using smaller markers. final touch change tooltip display gene Name.","code":"library(geneviewer) library(dplyr) # change the path to where you have saved the  # file or the directory containing all .gff files folder_path <- \"~/path/to/folder/\" gff <- read_gff(   folder_path,    fields = c(\"source\", \"type\", \"start\", \"end\", \"strand\", \"Name\")   ) %>%   dplyr::filter(type == \"CDS\")  # Add viral names virus_names <- c(   GU071086 = \"Marseillevirus\",    HQ113105.1 = \"Lausannevirus\",   KF261120 = \"Cannesvirus\",   KF483846 = \"Tunisvirus\" ) gff <- gff %>% mutate(Name = virus_names[filename])   View(gff) # Inspect the data frame in Rstudio GC_chart(gff,           start = \"start\",           end = \"end\",           strand = \"strand\",           cluster = \"Virus\",          height = \"400px\",          ) %>%   GC_title(     \"Marseilleviridae<\/i> viral genomes\",      height = \"40px\") %>%   GC_clusterLabel() %>%   GC_scale(axis_type = \"range\") %>%   GC_genes(     group = \"filename\",      stroke = \"none\",      marker_size = \"small\"     ) %>%   GC_tooltip(formatter = \"Gene:<\/b> {Name}\")"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGenBankFiles.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Loading Gene Clusters From Genbank Files","text":"tutorial demonstrates creating gene cluster visualizations GenBank files using geneviewer. guidance importing clusters FASTA files see: link. can obtain GenBank files containing genomic data variety platforms NCBI, Ensembl, UCSC, antiSMASH MIBiG. geneviewer designed handle GenBank files sources (please report compatibility issues Github), tutorial specifically aims replicate gene cluster visualization found MIBiG website.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGenBankFiles.html","id":"materials","dir":"Articles","previous_headings":"","what":"Materials","title":"Loading Gene Clusters From Genbank Files","text":".gbk files can downloaded MIBiG website following instructions directly geneviewer-tutorials repository.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGenBankFiles.html","id":"loading-genbank-file","dir":"Articles","previous_headings":"","what":"Loading GenBank file","title":"Loading Gene Clusters From Genbank Files","text":"GenBank files MIBiG include additional details, enabling us color-code genes function, use reproduce visualizations show website. Begin downloading GenBank file MIBiG website. tutorial use genbank file gene cluster BGC0000001. Simply click “Download GenBank file” link save file. can load file R using read_gbk function geneviewer. create list containing sections features found GenBank file. can inspect .gbk using View pane Rstudio (use View(gbk)) simply opening .gbk file text editor. visualization interested start end position gene well identifiers functions. can find FEATURES > CDS. Lets print first CDS see information contains. can bind information CDS data.frame using gbk_features_to_df function. code define feature keys interested bind data.frame. set process_region TRUE extract strand, start end region key.","code":"library(geneviewer) # change the path to where you have saved the file file_path <- \"~/path/to/file/BGC0000001.gbk\" gbk <- read_gbk(file_path) View(gbk) # Inspect the list in Rstudio CDS_1 <- gbk[[\"BGC0000001\"]][[\"FEATURES\"]][[\"CDS\"]][[1]]  df <- data.frame(values = CDS_1) df cds_df <- gbk_features_to_df(   gbk,    feature = \"CDS\",   keys = c(\"region\", \"gene\", \"protein_id\", \"gene_kind\", \"product\"),    process_region = TRUE   )"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGenBankFiles.html","id":"cluster-visualization","dir":"Articles","previous_headings":"","what":"Cluster Visualization","title":"Loading Gene Clusters From Genbank Files","text":"can see NA values gene_kind column replace “”. done ready make cluster visualization. make chart similar one find MIBiG website can add title, alter coloring appearance genes add scale. addition, alter tooltip display gene, product region hoover.","code":"# replace NA with \"other\" for gene_kind cds_df$gene_kind[is.na(cds_df$gene_kind)] <- \"other\"  # Make the cluster chart chart <- GC_chart(   cds_df,   start = \"start\",   end = \"end\",   group = \"gene_kind\",   strand = \"strand\",   height = \"130px\" ) chart colors <- list(   \"biosynthetic\" = \"#810E15\",    \"biosynthetic-additional\" = \"#F16D75\",    \"transport\" = \"#6495ED\",   \"regulatory\" = \"#2E8B57\",    \"other\" = \"#808080\" )  chart %>%   GC_genes(     marker = \"boxarrow\",     marker_size = \"small\"   ) %>%   GC_title(     \"BGC0000001: abyssomicin C biosynthetic gene cluster     from Verrucosispora maris<\/i> AB-18-032\",     align = \"left\",     titleFont = list(       fontSize = \"12px\"     )     ) %>%   GC_scale() %>%   GC_color(customColors = colors) %>%   GC_legend(order = names(colors)) %>%   GC_tooltip(     formatter = \"     Gene:<\/b> {gene}
     Product:<\/b> {product}
     Region:<\/b>{start} - {end}     \"   )"},{"path":"https://nvelden.github.io/geneviewer/articles/LoadGenBankFiles.html","id":"loading-multiple-genbank-files","dir":"Articles","previous_headings":"","what":"Loading Multiple GenBank files","title":"Loading Gene Clusters From Genbank Files","text":"functions read transfom .gbk files can also used load multiple .gbk files folder shown clusters side side. demonstrate can go cluster page BGC0000001 navigate “KnownClusterBlast” page. Click homologous clusters download .gbk files BGC0001694, BGC0001492, BGC0001288 BGC0000133. place .gbk files directory can load together done previously. now list .gbk files containing different sections features. can use gbk_features_to_df function make data.frame features. time besides CDS also make data.frame source can add Organism name genomic region title cluster. can now plot graph time specify “cluster” column identifier distinguish clusters add cluster labels titles.","code":"library(geneviewer) # change the path to the folder containing the .gbk files folder_path <- \"~/path/to/folder/\" gbk <- read_gbk(folder_path) View(gbk) # Inspect the list in Rstudio cds_clusters_df <- gbk_features_to_df(   gbk_list,    feature = \"CDS\",   keys = c(\"region\", \"gene\", \"protein_id\", \"gene_kind\", \"product\"),    process_region = TRUE   ) source_clusters_df <- gbk_features_to_df(gbk_list, feature = \"source\") #> Warning in gbk_features_to_df(gbk_list, feature = \"source\"): Feature source not #> found in cluster BGC0001004 #> Warning in gbk_features_to_df(gbk_list, feature = \"source\"): Feature source not #> found in cluster BGC0001204 #> Warning in gbk_features_to_df(gbk_list, feature = \"source\"): Feature source not #> found in cluster BGC0002124 # replace NA with \"other\" for gene_kind cds_clusters_df$gene_kind[is.na(cds_clusters_df$gene_kind)] <- \"other\"  colors <- list(   \"biosynthetic\" = \"#810E15\",    \"biosynthetic-additional\" = \"#F16D75\",    \"transport\" = \"#6495ED\",   \"regulatory\" = \"#2E8B57\",    \"other\" = \"#808080\" )  # Make the cluster chart GC_chart(   cds_clusters_df,   start = \"start\",   end = \"end\",   group = \"gene_kind\",   strand = \"strand\",   cluster = \"cluster\",   height = \"800px\" ) %>%     GC_clusterTitle(     y = 5,       title = paste0(\"\", source_clusters_df$organism, \"<\/i>: \", source_clusters_df$region),     align = \"left\",     titleFont = list(fontSize = 12),     ) %>%   GC_clusterLabel(names(gbk_list)) %>%   GC_genes(     marker = \"boxarrow\",     marker_size = \"small\"   ) %>%   GC_scaleBar(title = \"1kb\", scaleBarUnit = 1000) %>%   GC_color(customColors = colors) %>%   GC_legend(order = names(colors)) %>%   GC_tooltip(     formatter = \"     Gene:<\/b> {gene}
     ProteinID:<\/b> {protein_id}
     Product:<\/b> {product}
     Region:<\/b>{start} - {end}     \"   )"},{"path":"https://nvelden.github.io/geneviewer/articles/MUMMER.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Genome alignment using MUMmer","text":"tutorial guides process performing genome alignments using MUMmer, alignment tool widely used comparing genomic sequences. example align plasmids serveral species B. thuringiensis. Following alignment, ’ll show visualize results using geneviewer.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/MUMMER.html","id":"materials","dir":"Articles","previous_headings":"","what":"Materials","title":"Genome alignment using MUMmer","text":".gbk files can downloaded directly GenBank using accession numbers CP000486.1, CP009599.1, CP003188.1 CP009638.1. Alternatively, can obtain GenBank files including alignment files directly geneviewer-tutorials repository.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/MUMMER.html","id":"mummer-alignment","dir":"Articles","previous_headings":"","what":"MUMmer alignment","title":"Genome alignment using MUMmer","text":"MUMmer needs installed local machine execute alignments. detailed installation instructions, visit MUMmer website. MUMmer installed, can perform alignment using geneviewer mummer_alignment() function. default run alignment order files folder. Important MUMmer requires file paths without spaces. default, mummer_alignment() function perform pair wise alignments starting first file folder. adjust order files aligned, assign vector file names cluster variable. default nucleotide sequences translated proteins using “promer” “many--many” mapping alignment performed. suitable alignment method project, please carefully review MUMmer documentation. learn modify default settings, consult documentation running ?mummer_alignment(). alignment generates data frame details start end positions aligned region reference (cluster1) query (cluster2), along identity similarity scores. data frame can directly loaded GC_links() function.","code":"library(geneviewer) # Change the path to the folder where the .gbk files are saved folder_path <- \"~/path/to/folder/\" alignment <-    mummer_alignment(     path = folder_path,     cluster = NULL,     maptype = \"many-to-many\",     seqtype = \"protein\"   )"},{"path":"https://nvelden.github.io/geneviewer/articles/MUMMER.html","id":"synteny-gene-cluster-chart","dir":"Articles","previous_headings":"","what":"Synteny gene cluster chart","title":"Genome alignment using MUMmer","text":"map alignment onto genome, must first load cluster information .gbk files. detailed instructions, please refer tutorial Load Gene Cluster data GenBank Files. add extra column called “CDS” data used key color genes. can load cluster data GC_chart() alignment data GC_links() function. addition, change axis_type “range”, make genes little smaller add cluster labels. customization options see Get started. Important: gene cluster data like alignment data loaded order files folder. custom order used MUMer alignment make sure sort “cluster” column cluster data way.","code":"folder_path <- \"~/path/to/folder/\" gbk <- read_gbk(folder_path) cds_df <- gbk_features_to_df(   gbk,    feature = \"CDS\",   keys = c(\"region\", \"gene\", \"protein_id\", \"note\", \"product\")   ) cds_df$type <- \"CDS\" GC_chart(   data = cds_df,   group = \"cluster\",   strand = \"strand\",   cluster = \"cluster\" ) %>% GC_links(   data = alignment,   measure = \"identity\", # similarity/none ) %>% GC_scale(axis_type = \"range\") %>% GC_cluster(separate_strands = TRUE) %>% GC_genes(   group = \"type\",   marker_size = \"small\" ) %>%     GC_clusterLabel(   title = c(\"pALH1\", \"pBFQ\", \"F837_55\", \"pBFI_4\"),    width = 50   ) %>% GC_tooltip(   formatter = \"{protein_id}<\/b>
{start} - {end}\"  ) %>% GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/Transcripts.html","id":"intro","dir":"Articles","previous_headings":"","what":"Intro","title":"Visualizing gene Transcripts","text":"tutorial shows use biomaRt load transcript data Ensembl visualize using geneviewer. practical example, retrieve exon UTR regions five different splice variants BRCA1 gene display results geneviewer.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/Transcripts.html","id":"loading-transcript-data","dir":"Articles","previous_headings":"","what":"Loading Transcript data","title":"Visualizing gene Transcripts","text":"Transcript data BRCA1 gene can loaded using biomaRt package, Ensembl gene ID obtained Ensembl website. example, first load necessary libraries. Next, specify Ensembl gene ID BRCA1 establish connection Ensembl database using useMart(). Finally, retrieve transcript IDs associated BRCA1 gene using getBM() function. Now transcript IDs associated BRCA1 gene, can retrieve start end positions exons, well 5’ 3’ UTRs. Additionally, add strand information transcript. example, retrieve information first 5 transcript IDs. use getBM function retrieve start end positions feature separately. rename start end columns, allowing us combine results single data frame using bind_rows dplyr package. Finally, remove rows NA start column add strand information transcript. Now start, end strand information transcripts can visualize results using geneviewer GC_transcript function. Note intron positions calculated based exon positions. ensure exons recognized, type column feature name must specified include “exon” name. can customize chart adding title transcript name footer relative abundance transcript. change color, alter appearance specific features, explore many options, see Get Started guide GC_transcripts documentation running ?GC_transcripts console.","code":"library(biomaRt) library(geneviewer) library(dplyr)   ensembl_gene_id <- c(\"ENSG00000012048\") mart = useMart(\"ensembl\", dataset = \"hsapiens_gene_ensembl\")  # Retrieve all transcript IDs for the gene transcrips <- getBM(attributes = c(\"ensembl_gene_id\", \"ensembl_transcript_id\"),                               filters = \"ensembl_gene_id\",                               values = ensembl_gene_id,                               mart = mart) transcript_IDs <- transcrips$ensembl_transcript_id[1:5]  # Get exon details exon_attributes <- c(\"ensembl_transcript_id\", \"exon_chrom_start\", \"exon_chrom_end\") exon_results <- getBM(attributes = exon_attributes,                       filters = \"ensembl_transcript_id\",                       values = transcript_IDs,                       mart = mart) %>%   dplyr::mutate(type = \"exon\", start = exon_chrom_start, end = exon_chrom_end) %>%   dplyr::select(ensembl_transcript_id, type, start, end)  # Get 3' UTR details utr3_attributes <- c(\"ensembl_transcript_id\", \"3_utr_start\", \"3_utr_end\") utr3_results <- getBM(attributes = utr3_attributes,                       filters = \"ensembl_transcript_id\",                       values = transcript_IDs,                       mart = mart) %>%   dplyr::mutate(type = \"3_utr\", start = `3_utr_start`, end = `3_utr_end`) %>%   dplyr::select(ensembl_transcript_id, type, start, end)  # Get 5' UTR details utr5_attributes <- c(\"ensembl_transcript_id\", \"5_utr_start\", \"5_utr_end\") utr5_results <- getBM(attributes = utr5_attributes,                       filters = \"ensembl_transcript_id\",                       values = transcript_IDs,                       mart = mart) %>%   dplyr::mutate(type = \"5_utr\", start = `5_utr_start`, end = `5_utr_end`) %>%   dplyr::select(ensembl_transcript_id, type, start, end)  # Bind features transcript_attributes <- bind_rows(exon_results, utr3_results, utr5_results) %>%   filter(!is.na(start))  # Add strand transcript_strand <- getBM(attributes = c(\"ensembl_transcript_id\", \"strand\"),                            filters = \"ensembl_transcript_id\",                            values = transcript_IDs,                            mart = mart)   # Add transcript strand transcript_attributes <-    dplyr::left_join(     transcript_attributes,      transcript_strand,      by = \"ensembl_transcript_id\"     ) GC_chart(   data = transcript_attributes,    start = \"start\",   end = \"end\",   strand = \"strand\",   height = \"600px\" ) %>%   GC_transcript(     transcript = \"ensembl_transcript_id\",     type = \"type\"   ) GC_chart(   data = transcript_attributes,    height = \"600px\"   ) %>%   GC_transcript(     transcript = \"ensembl_transcript_id\",      strand = \"strand\",      type = \"type\",   ) %>%   GC_clusterTitle(     title = unique(transcript_attributes$ensembl_transcript_id),     titleFont = list(       fontSize = \"12px\"     )   ) %>%   GC_clusterFooter(     title = c(\"0.8%\", \"0.1%\", \"0.07%\", \"0.02%\", \"0.01%\"),     align = \"center\"   )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"installation","dir":"Articles","previous_headings":"","what":"Installation","title":"geneviewer","text":"geneviewer available GitHub","code":"# install.packages(\"devtools\") devtools::install_github(\"nvelden/geneviewer\")"},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"single-gene-cluster","dir":"Articles","previous_headings":"Cluster Visualization","what":"Single Gene Cluster","title":"geneviewer","text":"visualize single gene cluster, minimum requirements start end positions gene, typically named “start” “end”. addition group can defined used color coding genes used default categorical variable legend.","code":"# Example data for a single Gene cluster ophA_cluster <- subset(ophA_clusters, cluster == \"ophA\")  GC_chart(ophA_cluster,           start = \"start\",           end = \"end\",           group = \"class\",           height = \"150px\"          )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"multiple-gene-clusters","dir":"Articles","previous_headings":"Cluster Visualization","what":"Multiple Gene Clusters","title":"geneviewer","text":"visualizing multiple gene clusters, additional variable needed used define clusters (shown ‘cluster’ column ). example overall chart height set “300px”. Since two distinct gene clusters height cluster 150px.","code":"# Example data for two Gene clusters GC_chart(ophA_clusters,           start = \"start\",           end = \"end\",           group = \"class\",           cluster = \"cluster\",           height = \"300px\"          )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"styling","dir":"Articles","previous_headings":"Cluster Visualization","what":"Styling","title":"geneviewer","text":"customize overall appearance chart, can use style parameter, accepts list CSS style properties. styling specific elements individually, please refer corresponding functions listed .","code":"# Example data for two Gene clusters GC_chart(ophA_clusters,           start = \"start\",           end = \"end\",           group = \"class\",           cluster = \"cluster\",           height = \"200px\",          style = list(            border = \"1px solid black\",            backgroundColor = \"#FAEBD7\"            # Any other CSS style            )          )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"shiny","dir":"Articles","previous_headings":"","what":"Shiny","title":"geneviewer","text":"GC_chartOutput() renderGC_chart() functions enable visualize gene clusters within Shiny applications.","code":"# Load necessary libraries library(shiny) library(geneviewer)   # Define UI ui <- fluidPage(titlePanel(\"Omphalotin Gene Cluster Visualization\"),                 mainPanel(# Output for GC_chart                   GC_chartOutput(                     \"gcChart\", width = \"100%\", height = \"400px\"                   )))  # Define server logic server <- function(input, output) {   output$gcChart <- renderGC_chart({          GC_chart(       ophA_clusters,       cluster = \"cluster\",       group = \"class\"     ) %>%       GC_clusterTitle(title = c(\"O. olearius<\/i>\", \"D. bispora<\/i>\")) %>%       GC_labels(\"name\") %>%       GC_legend(position = \"bottom\") %>%       GC_scaleBar() %>%       GC_clusterLabel(title = \"ophA\")        }) }  # Run the application shinyApp(ui = ui, server = server)"},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"specific-clusters","dir":"Articles","previous_headings":"Selections","what":"Specific Clusters","title":"geneviewer","text":"Customization functions default set alter styling gene clusters across chart. select specific cluster one can use cluster variable available customization functions. can select cluster either ’s name number. example y position adjusted first cluster shifting labels cluster.","code":"GC_chart(ophA_clusters, cluster = \"cluster\", group = \"class\", height = \"350px\") %>%   GC_title(title = \"ophA Gene Clusters\") %>%   GC_labels(label = \"name\", cluster = \"ophA\", y = 18) %>%   GC_labels(label = \"name\", cluster = 2)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"individual-items","dir":"Articles","previous_headings":"Selections","what":"Individual Items","title":"geneviewer","text":"apply styling particular item within gene cluster, itemStyle variable can used. variable, accessible customization functions, requires list specifies index number desired item along intended styling attributes. ’s important note indexing itemStyle begins 0, following zero-based numbering system. example , 3rd label ophA cluster styled red color bold font. code also customizes labels cluster 2, 5th label similarly styled red bold, 4th label’s position adjusted.","code":"GC_chart(ophA_clusters, cluster = \"cluster\", group = \"class\", height = \"300px\") %>%   GC_title(title = \"ophA Gene Clusters\", height = \"30px\") %>%   GC_labels(label = \"name\",              cluster = \"ophA\",              itemStyle =                list(                 list(index = 2, fill = \"red\", fontWeight = \"bold\")                 )             ) %>%   GC_labels(     label = \"name\",      cluster = 2,     itemStyle =                list(                 list(index = 4, fill = \"red\", fontWeight = \"bold\"),                 list(index = 3, y = 10, x = -5)                 )     )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"cluster","dir":"Articles","previous_headings":"","what":"Cluster","title":"geneviewer","text":"GC_cluster function can used style adjust margins specific clusters. example set different background color cluster decrease left right margins 25px. Note margins title legend adjusted. adjust well easiest use GC_grid function adjust margins elements .","code":"GC_chart(   ophA_clusters,   group = \"class\",   cluster = \"cluster\",   height = \"300px\"    ) %>%   GC_title(\"Adjust margins of GC clusters\", align = \"left\", height = \"40px\") %>%   GC_cluster(margin = list(left = 25, right = 25)) %>%   GC_cluster(cluster = 1, style = list(backgroundColor = \"green\")) %>%   GC_cluster(cluster = 2, style = list(backgroundColor = \"red\"))"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"separation-of-forward-and-reverse-strands","dir":"Articles","previous_headings":"Cluster","what":"Separation of Forward and Reverse strands","title":"geneviewer","text":"Forward reverse strands can separated distinct tracks. example forward reverse strands separated second cluster. vertical spacing slightly increased (default = 0). Note: GC_cluster() function must called setting genes, labels coordinates proper effect.","code":"GC_chart(   ophA_clusters,   group = \"name\",   cluster = \"cluster\",   height = \"350px\"    ) %>%    GC_labels() %>%   GC_cluster(separate_strands = TRUE, strand_spacing = 3) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"prevent-gene-overlap","dir":"Articles","previous_headings":"Cluster","what":"Prevent Gene Overlap","title":"geneviewer","text":"prevent gene overlaps, genes automatically separated distinct tracks. GC_cluster function track-based separation can switched spacing tracks can adjusted. example track switched first cluster spacing second cluster increased 40 50. Note: Setting separate_strands prevent_gene_overlap TRUE supported moment.","code":"GC_chart(   subset(human_hox_genes, cluster %in% c(\"HOXA\", \"HOXB\")),   group = \"name\",   cluster = \"cluster\",   height = \"300px\"    ) %>%    GC_labels(label = \"name\", adjustLabels = FALSE) %>%   GC_labels(label = \"name\",              cluster = 2,              itemStyle = list(list(index = 5, x=10))             ) %>%   GC_cluster(prevent_gene_overlap = TRUE, overlap_spacing = 30) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"grid","dir":"Articles","previous_headings":"","what":"Grid","title":"geneviewer","text":"GC_grid() function can used modify grid chart specific clusters. example top bottom margins increased left right margins decreased 50px default 25px. Clusters can shown side side setting direction row adjusting width cluster.","code":"GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\",          style = list(backgroundColor = \"red\"),          height = \"300px\"          ) %>%   GC_title(     \"Adjusting Margins of a GC_chart\",      align = \"left\",      y = 15,      style = list(backgroundColor = \"yellow\",                   align = \"left\")     ) %>%   GC_cluster(style = list(backgroundColor = \"green\")) %>%   GC_legend(TRUE, style = list(backgroundColor = \"yellow\")) %>%   GC_grid(margin = list(top = 50, bottom = 50, left = 25, right = 25)) GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"250px\") %>%   GC_grid(direction = \"row\", margin = list(left = 15, right = 15)) %>%   GC_clusterTitle(c(\"Omphalotus Olearius<\/i>\", \"Dendrothele Bisporus<\/i>\")) %>%   GC_legend(position = \"top\") %>%   GC_grid(     cluster = c(1,2),      width = \"50%\",     height = \"50%\"   )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"genes","dir":"Articles","previous_headings":"","what":"Genes","title":"geneviewer","text":"GC_genes() function can used custom style genes. example stroke stroke width altered can take valid CSS style. color coding set according group GC_chart() function. Changing color scheme best done GC_color() function (see: Colors section) uniformly change colors genes legend. default genes displayed arrows. alter appearance one can use marker marker_size variables. Beside default arrow marker one can use boxarrow, box, rbox cbox. can set marker small, medium (default) large. finer control one can use markerHeight variable overwrite marker_size variable. addition can change position markers using x y variables. case arrow boxarrow markers can also alter arrowhead using arrowheadWidth arrowheadHeight variables.","code":"GC_chart(ophA_cluster, cluster = \"cluster\", group = \"class\", height = \"150px\") %>%   GC_genes(     show = TRUE,     stroke = \"grey\",     strokeWidth = 2     # Any other CSS style   ) %>%    GC_color(colorScheme = \"schemeAccent\") %>%    GC_legend() GC_chart(ophA_cluster, cluster = \"cluster\", group = \"class\", height = \"100px\") %>%   GC_genes(marker = \"arrow\", marker_size = \"small\") %>%   GC_clusterLabel(\"arrow\") %>%    GC_legend(FALSE) GC_chart(ophA_cluster, cluster = \"cluster\", group = \"class\", height = \"100px\") %>%   GC_genes(     y = 55,     marker = \"arrow\",      markerHeight = 10,     arrowheadHeight = 15,     arrowheadWidth = 15     ) %>%   GC_clusterLabel(\"customized arrows\") %>%    GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"gene-alignment","dir":"Articles","previous_headings":"","what":"Gene alignment","title":"geneviewer","text":"GC_align() function can used align specific gene across clusters. example , specify column contains gene identifiers vertically align gene across clusters left. Please note gene identifier used alignment must across clusters unique within cluster.","code":"GC_chart(ophA_clusters, cluster = \"cluster\", group = \"class\", height = \"150px\") %>%    GC_align(      id_column = \"class\",       id = \"NTF2-like\",      align = \"left\" # center / right      ) %>%    GC_legend(TRUE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"gene-normalization","dir":"Articles","previous_headings":"","what":"Gene normalization","title":"geneviewer","text":"GC_normalize function can used normalize genomic coordinates set genes within cluster, ensuring genes evenly spaced along entire range cluster. example normalize genes first cluster even spacing genes preserving original length. Optionally, custom spacing genes can set using gap variable. Note: Normalization adjust start end positions genes, causing differ original coordinates. display original start end positions tooltip, formatter can updated use original_start original_end values. can adjust spacing specific genes using custom_gaps variable. example , normalize spacing genes first cluster, set uniform gap width genes, increase gap 1.5x genes ophC ophB2.","code":"GC_chart(ophA_clusters, cluster = \"cluster\", group = \"class\", height = \"150px\") %>%    GC_normalize(      group = \"class\",       cluster = 1, # By default all clusters are normalized      gap = NULL, # 0-1      preserve_gene_length = TRUE      ) %>%   # Update tooltip   GC_tooltip(     cluster = 1,     formatter = \"Start:<\/b> {original_start}
End:<\/b> {original_end}\"   ) %>%   GC_legend(FALSE) GC_chart(ophA_clusters, cluster = \"cluster\", group = \"class\", height = \"280px\") %>%    GC_normalize(      group = \"name\",       cluster = 1, # By default all clusters are normalized      gap = 0.01, # 0-1      custom_gaps = list(ophC = 1.5, ophB2 = 1.5),      preserve_gene_length = FALSE      ) %>%   GC_labels(label = \"name\") %>%   # Update tooltip   GC_tooltip(     cluster = 1,     formatter = \"Start:<\/b> {original_start}
End:<\/b> {original_end}\"   ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"blastp","dir":"Articles","previous_headings":"","what":"BlastP","title":"geneviewer","text":"protein_blast() function can used perform BlastP alignment clusters. information see Cluster comparison using BlastP tutorial.","code":"BlastP_results <-    protein_blast(     data, # or path to folder containing .gbk files     query, # The name of the query cluster to be used for BLAST comparisons.     id = \"protein_id\", # The name of the column that contains the gene identifiers.     start = \"start\",     end = \"end\",     cluster = \"cluster\",     genes = NULL, #Vector of protein IDs to include for BlastP analysis.     identity = 30,     parallel = TRUE )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"transcripts","dir":"Articles","previous_headings":"","what":"Transcripts","title":"geneviewer","text":"GC_transcript() function can used visualize transcripts. requires setting transcript column unique IDs transcript type column identifying whether feature “UTR”, “exon”. Optionally, can also set direction specifying strand column. Please note introns calculated based exon positions. wide range options customize exons, introns UTRs. options see documentation running ?GC_transcript(). Junctions can added transcripts using Arc annotation. example setting custom colors grouping “type” specifying colors using customColors. introns, exons, UTRs, labels can styled using styleIntrons, styleExons, styleUTRs, labelOptions variables respectively. itemStyle combination selection variable allows customization individual exons, introns, UTRs within specific transcripts.","code":"transcript_data <- data.frame(   transcript = c(\"transcript1\", \"transcript1\", \"transcript1\", \"transcript1\",                  \"transcript2\", \"transcript2\", \"transcript2\"),   type = c(\"5_utr\", \"exon\", \"exon\", \"3_utr\",            \"5_utr\", \"exon\", \"3_utr\"),   start = c(1, 101, 201, 301,             1, 101, 301),   end = c(50, 150, 250, 350,           50, 150, 350),   strand = rep(\"forward\", 7) )  GC_chart(   transcript_data,    start = \"start\",   end = \"end\",   height = \"200px\") %>% GC_transcript(   transcript = \"transcript\",    strand = \"strand\",  ) GC_chart(   transcript_data,    start = \"start\",   end = \"end\",   height = \"200px\"   ) %>%   GC_transcript(     group = \"type\",     customColors =        list(         exon = \"green\",         intron = \"blue\",         `5_utr` = \"black\",         `3_utr` = \"grey\"       )     ) GC_chart(transcript_data, height = \"200px\") %>%   GC_transcript(     styleIntrons =        list(       strokeWidth = 2,       markerHeight = 60       # Any other CSS style       ),     styleExons =        list(         markerSize = \"small\",         fill = \"none\",         strokeWidth = 2,         stroke = \"red\"         # Any other CSS style       ),     styleUTRs = list(       marker = \"boxarrow\",       markerSize = \"small\",       fill = \"green\"       # Any other CSS style     ),     labelOptions = list(       show = TRUE,       xOffset = 0,       yOffset = 0,       fontSize = \"10px\",       fontWeight = \"bold\"       # Any other CSS style     )   ) GC_chart(   transcript_data,    start = \"start\",   end = \"end\",   height = \"200px\"   ) %>%   GC_transcript(     transcript = \"transcript\",     selection = 1,     itemStyleExons =        list(         list(index = 0, fill = \"red\")       )   ) %>%   GC_transcript(     transcript = \"transcript\",     selection = 2,     itemStyleIntrons =      list(       list(index = 1, stroke = \"red\", strokeWidth = 2)     )   )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"links","dir":"Articles","previous_headings":"","what":"Links","title":"geneviewer","text":"get_links GC_links() functions can used add links genes. example, initially create chart object. Subsequently, generate links among clusters. achieved specifying grouping column generate links value pairs different clusters. Using value1 value2 variables get_links function can generate links specific genes. case 2 clusters can use cluster variable allows specify clusters generate links . “identity” “similarity” column can added data used measure set color intensity links. addition links labels can styled using linkStyle labelStyle variable. data parameter allows load data frame defines links genomic regions start end positions, rather linking specific genes. can include “identity” “similarity” column used set color intensity links.","code":"# Generate chart object chart <- GC_chart(   ophA_clusters,    cluster = \"cluster\",    group = \"class\",    height = \"250px\") %>%   GC_legend(FALSE)  # Add links to chart chart %>% GC_links(\"class\") # Add links to chart chart %>%    GC_links(     \"name\",      value1 = c(\"ophB1\", \"ophC\"),      value2 = c(\"dbophB1\", \"dbophC\"),     cluster = c(1,2)     ) %>%    GC_labels(\"name\") ophA_clusters$identity <- sample(1:100, size = nrow(ophA_clusters), replace = TRUE)  ophA_clusters$identity[ophA_clusters$cluster == \"ophA\"] <- NA  chart <- GC_chart(   ophA_clusters,    cluster = \"cluster\",    group = \"class\",    height = \"250px\") %>%   GC_links(     \"class\",      value1 = c(\"Methyltransferase\", \"Prolyloligopeptidase\"),      value2 = c(\"Methyltransferase\", \"Prolyloligopeptidase\"),     inverted_color = \"green\",      measure = \"identity\", # similarity / none     label = TRUE,     curve = FALSE,     color_bar = TRUE,     colorBarOptions = list(        x = 0,        y = 24,        width = 10,        height = 60,        labelOptions = list(          fontSize = 8,          xOffset = 2,          yOffset = 0          # Any other CSS style        ),        titleOptions = list(          fontSize = 10,          xOffset = 2,          yOffset = 0          # Any other CSS style        ),        barOptions = list(          stroke = \"#000\",          strokeWidth = 0.5,          opacity = 1          # Any other CSS style        )      ),     linkStyle = list(       stroke = \"black\",       strokeWidth = 0.5       # Any other CSS style     ),     labelStyle = list(       fill = \"red\"       # Any other CSS style     )     ) %>%    GC_legend(TRUE)  chart links_data <- data.frame(   start1 = c(5000, 16000),   end1 =  c(9000, 19000),   start2 = c(20000, 42000),   end2 = c(25000, 32000),   cluster1 = c(\"ophA\",\"ophA\"),   cluster2 = c(\"dbophA\", \"dbophA\"),   identity = c(20, 100),   similarity = c(10, 90) ) # Add links to chart GC_chart(   ophA_clusters,    cluster = \"cluster\",    group = \"class\",    height = \"250px\") %>%    GC_links(     data = links_data,     measure = \"identity\"     )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"sequence","dir":"Articles","previous_headings":"","what":"Sequence","title":"geneviewer","text":"sequence line GC_sequence() function initially presented solid black line, can customized sequenceStyle option. Additionally, markerStyle option allows adjusting style break markers.","code":"GC_chart(   ophA_clusters, group = \"class\",   cluster = \"cluster\",   height = \"150px\") %>%   GC_sequence(     show = TRUE,     cluster = NULL,     y = 50,     sequenceStyle = list(       stroke = \"grey\",       strokeWidth = 1       # Any other CSS style     ),     markerStyle = list(       stroke = \"grey\",       strokeWidth = 1,       gap = 3,       tiltAmount = 5       # Any other CSS style     )   ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"labels","dir":"Articles","previous_headings":"","what":"Labels","title":"geneviewer","text":"gene cluster one can add title, gene labels, cluster label footer shown example . adjust positioning labels, x, y, align variables can used. Note example, GC_labels() employed twice: initially, sets labels uniformly gene clusters, specifically adjusts fourth eight label (considering index starts 0) cluster 2, ensure overlap. adjust position styling specific labels one can use cluster itemStyle variables. cluster variable one can select specific cluster name number. Using itemStyle variable one can provide list index number specific label styles applied . Note index itemStyle starts 0.","code":"GC_chart(ophA_clusters,           start = \"start\",           end = \"end\",           group = \"class\",           cluster = \"cluster\",           height = \"450px\"          ) %>%   GC_clusterTitle(     title = c(\"Omphalotus Olearius<\/i>\", \"Dendrothele Bisporus<\/i>\"),      titleFont = list(fontWeight = \"normal\")     ) %>%   GC_labels(\"name\") %>%   GC_clusterLabel(title = unique(ophA_clusters$cluster)) %>%   GC_clusterFooter(     x = 100,     title = c(\"Nr. of Genes: 7\", \"Nr. of Genes: 10\"),      subtitle = c(\"Locus: 2522 - 21,484\", \"Locus 19,236 - 43,005\")     ) %>%   GC_legend(position=\"top\") GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"360px\") %>%   GC_clusterTitle(     c(\"Omphalotus Olearius<\/i>\", \"Dendrothele Bisporus<\/i>\"),      position = \"left\",      x = 20) %>%   GC_labels(\"name\", y = 20) %>%   GC_labels(\"name\",              cluster = 2,              y = 20,              itemStyle =                list(                 list(index = 3, y = 52),                 list(index = 7, y = 52)                 )             ) %>%   GC_clusterFooter(     title = c(\"Nr. of Genes: 7\", \"Nr. of Genes: 10\"),      subtitle = c(\"Locus: 2522 - 21,484\", \"Locus 19,236 - 43,005\"),      align = \"center\"     ) GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"360px\") %>%   GC_labels(\"name\", y = 20) %>%   GC_labels(\"name\",              cluster = 2,              y = 20,             itemStyle = list(               list(index = 3, y = 52, fill = \"red\"),               list(index = 7, y = 52, fill = \"red\")               )             )"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"annotations","dir":"Articles","previous_headings":"","what":"Annotations","title":"geneviewer","text":"GC_annotation function can used add annotations specified clusters within GC chart. types annotations available : text, textMarker, line, arrow, symbol, rectangle, promoter, terminator. Annotations placed specifying type followed type specific parameters. shown example multiple annotations type can placed providing list values. GC_trackMouse() function can used track mouse coordinates hoovering chart makes easy determine x y positions place annotation.","code":"GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"300px\") %>%   GC_annotation(     cluster = 1,     type = \"text\",     text = \"Gene 1\",     x = 2970,     y = 60   ) %>%    GC_annotation(     cluster = 2,     type = \"text\",     text = c(\"Gene 1\", \"Gene 2\", \"Gene 3\"),     x = c(19400, 22200, 25600),     y = 60   ) %>%   GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"text","dir":"Articles","previous_headings":"Annotations","what":"Text","title":"geneviewer","text":"shows example options place text annotation. text, x y variables can also take list values.","code":"GC_chart(ophA_cluster, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_annotation(     cluster = 1,     type = \"text\",      text = \"Gene 1\",     x = 2970,     y = 58,     style = list(       fontSize = \"10px\",       fontStyle = \"normal\",       fontWeight = \"normal\",       textDecoration = \"none\",       fontFamily = \"sans-serif\",       cursor = \"default\"       # Any other CSS style     )    ) %>%   GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"text-marker","dir":"Articles","previous_headings":"Annotations","what":"Text Marker","title":"geneviewer","text":"shows example options place text Marker. exception styles variables can also take list values. default x1 x2 NULL position used horizontal placement.","code":"GC_chart(ophA_cluster, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_annotation(     cluster = 1,     type = \"textMarker\",      text = \"Gene 1\",     x1 = NULL,     y1 = 66,     x2 = NULL,     y2 = 50,     position = 9300,     labelX = 0,     labelY = 0,     showArrow = FALSE,     arrowSize = 8,     textStyle = list(       fontSize = \"10px\",       fontFamily = \"sans-serif\",       fill = \"black\",       textAnchor = \"middle\"     ),     arrowStyle = list(       fill = \"black\"     ),     lineStyle = list(       stroke = \"black\",       strokeWidth = 1     )   ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"promoter-terminator","dir":"Articles","previous_headings":"Annotations","what":"Promoter / Terminator","title":"geneviewer","text":"shows example options place promoter. exception styles variables can also take list values.","code":"GC_chart(ophA_cluster, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_annotation(     cluster = 1,     type = \"promoter\", # terminator     x = 9300,     y = 50,      direction = \"forward\", # reverse     style = list(       fill = \"none\",       stroke = \"black\",       strokeWidth = 1       # Any other CSS style     ),     rotation = 0,     scale = 1   ) %>%    GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"symbol","dir":"Articles","previous_headings":"Annotations","what":"Symbol","title":"geneviewer","text":"shows example options place symbol. Supported symbols circle, cross, diamond, square, star, triangle, wye. exception styles variables can also take list values.","code":"GC_chart(ophA_cluster, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_annotation(     cluster = 1,     type = \"symbol\", # circle/cross/diamond/square/star/triangle/wye     symbol = \"circle\",      x = 9300,     y = 50,      size = 64,     rotation = 0,     style = list(       fill = \"black\",       stroke = \"black\",       strokeWidth = 2       # Any other CSS style       )     ) %>%    GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"arrow","dir":"Articles","previous_headings":"Annotations","what":"Arrow","title":"geneviewer","text":"shows example options place arrow. exception styles variables can also take list values.","code":"GC_chart(ophA_cluster, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_annotation(     cluster = 1,     type = \"arrow\",     x1 = 9300,     y1 = 70,     x2 = 9300,     y2 = 50,     arrowSize = 8,     arrowStyle = list(       fill = \"black\"       # Any other CSS style     ),     lineStyle = list(       stroke = \"black\",       strokeWidth = 1       # Any other CSS style     )    ) %>%    GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"line","dir":"Articles","previous_headings":"Annotations","what":"Line","title":"geneviewer","text":"shows example options place line. exception styles variables can also take list values.","code":"GC_chart(ophA_cluster, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_annotation(     cluster = 1,     type = \"line\",     x1 = 9300,     y1 = 70,     x2 = 9300,     y2 = 50,     style = list(       stroke = \"black\",       strokeWidth = 1       # Any other CSS styles     )   ) %>%    GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"arc","dir":"Articles","previous_headings":"Annotations","what":"Arc","title":"geneviewer","text":"shows example options place arcs.","code":"transcript_data <- data.frame(   transcript = c(\"transcript1\", \"transcript1\", \"transcript1\", \"transcript1\"),   type = c(\"5_utr\", \"exon\", \"exon\", \"3_utr\"),   start = c(1, 101, 201, 301),   end = c(50, 150, 250, 350),   strand = rep(\"forward\", 4) )  GC_chart(   transcript_data,    start = \"start\",   end = \"end\",   height = \"200px\") %>% GC_transcript(   transcript = \"transcript\",    strand = \"strand\",  ) %>%   GC_annotation(     cluster = NULL,     type = \"arc\",     x1 = c(150, 50),                        y1 = c(50),                       x2 = c(301, 201),                      y2 = c(50),                       midY = c(80, 20),                     stroke = c(\"black\"),              strokeWidth = c(0.8, 0.1),              labelX = c(0),                    labelY = c(0),                    text = c(0.8, 0.1),                    lineStyle = list(       # Any other CSS styles     ),     textStyle = list(       fontSize = \"10px\",                fontFamily = \"sans-serif\",        fill = \"black\",                  textAnchor = \"middle\"             # Any other CSS styles     )   ) %>%    GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"square","dir":"Articles","previous_headings":"Annotations","what":"Square","title":"geneviewer","text":"shows example options place square. rotation variable can also take list values.","code":"GC_chart(ophA_cluster, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_annotation(     cluster = 1,     type = \"rectangle\",     rotation = 0,     position =        list(         list(c(9200, 60), c(11100, 40)),         list(c(11700, 60), c(12900, 40))         ),     style = list(       stroke = \"black\",       strokeWidth = 1       # Any other CSS styles     )   ) %>%    GC_legend(FALSE) %>%   GC_trackMouse()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"colors","dir":"Articles","previous_headings":"","what":"Colors","title":"geneviewer","text":"color legend genes can controlled GC_color function using colorScheme customColors variables.","code":""},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"colorscheme","dir":"Articles","previous_headings":"Colors","what":"colorScheme","title":"geneviewer","text":"Defines predefined color scheme legend, “schemeCategory10” “schemeAccent” D3.js. Supported schemes include: schemeCategory10: array ten categorical colors. schemeAccent: array eight categorical colors. schemeDark2: array eight categorical colors. schemePaired: array twelve categorical colors. schemePastel1: array nine categorical colors. schemePastel2: array eight categorical colors. schemeSet1: array nine categorical colors. schemeSet2: array eight categorical colors. schemeSet3: array twelve categorical colors. schemeTableau10: array ten categorical colors, originally created Tableau.","code":"GC_chart(ophA_cluster, group = \"class\", height = \"100px\") %>%   GC_color(colorScheme = \"schemeAccent\")"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"customcolors","dir":"Articles","previous_headings":"Colors","what":"customColors","title":"geneviewer","text":"customColors parameter specifies colors group legend. accepts either vector colors named list direct mapping, list(\"Class1\" = \"#FF5733\", \"Class2\" = \"#33CFFF\"). Using list colors: Using named list colors; ensure color changes take effect, GC_color function call must placed function calls. example , custom_colors overwritten color settings GC_genes function. Therefore, always place GC_color function call last.","code":"# Pass a list of Colors custom_colors <- c(\"#F8766D\",\"#00BA38\",\"#619CFF\",\"#F564E3\",\"#FFC61E\",\"#00BFC4\")  GC_chart(ophA_cluster, group = \"class\", height = \"100px\") %>%   GC_color(customColors = custom_colors ) # Pass a list of Colors custom_colors <- c(\"#D62728\", \"#2CA02C\", \"#1F77B4\", \"#9467BD\", \"#FF7F0E\", \"#17BECF\")  # Create a named list of colors named_vector <- setNames(custom_colors, unique(ophA_cluster$class)) custom_colors <- as.list(named_vector)  GC_chart(ophA_cluster, group = \"class\", height = \"100px\") %>%   GC_color(customColors = custom_colors ) # Pass a list of Colors custom_colors <- c(\"#D62728\", \"#D62728\", \"#D62728\", \"#D62728\", \"#D62728\", \"#D62728\")  # Create a named list of colors named_vector <- setNames(custom_colors, unique(ophA_cluster$class)) custom_colors <- as.list(named_vector)  GC_chart(ophA_cluster, group = \"class\", height = \"100px\") %>%   GC_color(customColors = custom_colors ) %>%   GC_genes() %>%   GC_legend()"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"legend","dir":"Articles","previous_headings":"","what":"Legend","title":"geneviewer","text":"GC_legend() function can used show / hide customize legend. default legend shown bottom. example shows GC_function() default settings. example advanced customization shown changing order, size, position appearance legend. color changed using GC_color function simultaneously adjusts colors legend genes.","code":"GC_chart(   ophA_clusters,    group = \"class\",    cluster = \"cluster\",   height = \"200px\") %>%  GC_legend(     show = TRUE,     position = \"bottom\", #top (left and right no supported for now)     orientation = \"horizontal\", #vertical     x = 0,     y = 0,     margin = list(top = 0, left = 50, bottom = 0,  right = 50),     width = NULL,     adjustHeight = TRUE,     order = list(),     style = list(       #backgroundColor = \"#0000\"       # Additional CSS styles     ),     positions = \"bottom\",     legendOptions = list(       cursor = \"pointer\",       colorScheme = NULL,       customColors = NULL        # Additional CSS styles     ),     legendTextOptions = list(       cursor = \"pointer\",       textAnchor = \"start\",       dy = \".35em\",       fontSize = \"12px\",       fontFamily = \"sans-serif\",       fill = \"black\"       # Additional CSS styles     )   ) GC_chart(   ophA_clusters,    group = \"class\",    cluster = \"cluster\",   height = \"200px\") %>%  GC_legend(     y = 10,     position = \"top\",     width = \"60%\",     order = sort(unique(ophA_clusters$class)),     legendTextOptions = list(       fontSize = \"14px\"     ),     legendOptions = list(stroke = \"black\", strokeWidth = \"2px\")   ) %>%    GC_color(colorScheme = \"schemePaired\")"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"scale","dir":"Articles","previous_headings":"","what":"Scale","title":"geneviewer","text":"GC_scale() function utilized adjusting chart’s scale. padding parameter can used add extra space start end cluster. visibility scale can controlled hidden parameter, , set TRUE, hides axis. y parameter can used adjust horizontal position axis (1 bottom 100 top).","code":"GC_chart(ophA_cluster, group = \"class\", height = \"100px\") %>%   GC_scale(     padding = 2,     hidden = FALSE,     axisType = \"bottom\",     y = NULL) %>%    GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"automatic-scale-breaks","dir":"Articles","previous_headings":"Scale","what":"Automatic Scale Breaks","title":"geneviewer","text":"GC_scale() function, parameters scale_breaks, scale_break_threshold, scale_break_padding can used avoid issues widely spaced genes within cluster. Setting scale_breaks TRUE introduces breaks genomic scale avoid long empty stretches. scale_break_threshold defines spacing percentage genes needed activate breaks. scale_break_padding controls padding around breaks. given example, scale break introduced cases intergenic region exceeds 20% total range gene cluster. Additionally, padding 1% added left right sides break.","code":"# With scale breaks GC_chart(ophA_cluster, group = \"class\", height = \"100px\") %>%   GC_scale(     scale_breaks = TRUE,     scale_break_threshold = 20,     scale_break_padding = 1   ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"manual-scale-adjustments","dir":"Articles","previous_headings":"Scale","what":"Manual Scale Adjustments","title":"geneviewer","text":"default minimum maximum genes start end positions used position genes along sequence. use start end parameters, values can adjusted. Scale breaks can added manually using breaks parameter. provided example range altered providing custom start end values. Additionally, scale break introduced remove extensive intergenic region exists gene 2 gene 3.","code":"GC_chart(   ophA_cluster,    start = \"start\",    end = \"end\",    group = \"class\",    height = \"100px\") %>%   GC_scale(     start = 1522,      end = 22484,     breaks =        list(         list(start = 5486, end = 9336)       )     ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"reverse-scale","dir":"Articles","previous_headings":"Scale","what":"Reverse Scale","title":"geneviewer","text":"scale can reversed setting reverse = TRUE.","code":"GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"200px\") %>%   GC_scale(cluster = 1, reverse = FALSE, ticksCount = 10) %>%   GC_scale(cluster = 2, reverse = TRUE, ticksCount = 10)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"shared-genomic-scale","dir":"Articles","previous_headings":"Scale","what":"Shared genomic scale","title":"geneviewer","text":"setting axis_type range, can standardize axis across clusters, shifting precise genomic coordinates unified scale. scale based widest span observed among clusters, starting 0 extending endpoint cluster covering largest range. Warning: using shared axis options like setting breaks reversing scale might work anymore.","code":"GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"200px\") %>%   GC_scale(axis_type = \"range\")"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"styling-1","dir":"Articles","previous_headings":"Scale","what":"Styling","title":"geneviewer","text":"scale can styled using tickStyle, textStyle lineStyle options. can pass valid CSS styles respective styling list(). amount ticks can specified using ticksCount option. Alternatively, ticks can manually specified using tickValues parameter. ticksFormat parameter used define numerical labels tick marks formatted (see: link).","code":"GC_chart(ophA_cluster, group = \"class\", height = \"100px\") %>%   GC_scale(     ticksFormat = \".2s\", # Default: \",.0f\"     tickValues = c(ophA_cluster$start, ophA_cluster$end),     #ticksCount = 10,     tickStyle =        list(         stroke = \"black\",          strokeWidth = 2,          lineLength = 12         # Any other CSS styles         ),     textStyle =        list(         y = 15,         fill = \"black\",          fontSize = \"8px\",          fontFamily = \"Arial\"         # Any other CSS styles         ),     lineStyle = list(       stroke = \"black\",        strokeWidth = 2       # Any other CSS styles       )   ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"coordinates","dir":"Articles","previous_headings":"","what":"Coordinates","title":"geneviewer","text":"Gene coordinates can displayed GC_coordinates() function. overlapping coordinates occur, , default, shifted top axis clearer visualization. default overlapThreshold parameter set 20. style ticks text can customized using tickStyle textStyle variables. scale can changed using GC_scale() function. instance want use reverse scale displaying coordinates can set GC_scale hidden. default, start end positions gene indicated coordinates. However, can customize providing values top bottom ticks, using tickValuesTop tickValuesBottom options. ticksFormat parameter used define numerical labels tick marks formatted (see: link).","code":"dbophA_cluster <- subset(ophA_clusters, cluster == \"dbophA\")  GC_chart(dbophA_cluster, group = \"class\",height = \"100px\") %>%   GC_coordinates(   rotate = -45,   yPositionTop = 55,   yPositionBottom = 45,   overlapThreshold = 20   ) %>%   GC_legend(FALSE) GC_chart(dbophA_cluster, group = \"class\",height = \"100px\") %>%   GC_scale(hidden = TRUE, reverse = TRUE) %>%   GC_coordinates(    tickStyle = list(stroke = \"grey\", strokeWidth = 1, lineLength = 10),    textStyle = list(fill = \"gray\", fontSize = \"10px\", fontFamily = \"Arial\", cursor = \"default\")    ) %>%    GC_legend(FALSE) GC_chart(dbophA_cluster, group = \"class\",height = \"100px\") %>%   GC_coordinates(     tickValuesTop = c(27371, 28937),     tickValuesBottom = c(25288, 27217),     ticksFormat = \".2s\", # Default: \",.0f\"    ) %>%    GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"scalebar","dir":"Articles","previous_headings":"","what":"Scalebar","title":"geneviewer","text":"scalebar can added gene cluster chart using GC_scaleBar(). function, default, displays scale bar 1000 base pairs (bp) labeled “1kb”. scalebar’s position label can customized using x, y, labelPosition parameters. CSS styles can added modify labels. appearance scalebar line ticks adjustable scaleBarLine scaleBarTick options.","code":"GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_scaleBar(     title = \"1kb\",     scaleBarUnit = 1000     ) %>%   GC_legend(FALSE) GC_chart(ophA_clusters, group = \"class\", cluster = \"cluster\", height = \"150px\") %>%   GC_scaleBar(     title = \"1kb\",     scaleBarUnit = 1000,     cluster = NULL,     x = 0,     y = 0,     labelStyle = list(       labelPosition = \"left\",       fontSize = \"10px\",       fontFamily = \"sans-serif\",       fill = \"black\",           cursor = \"default\"        # Any other CSS style for the label     ),     textPadding = 2,     scaleBarLineStyle = list(       stroke = \"black\",       strokeWidth = 1       # Any other CSS style for the line     ),     scaleBarTickStyle = list(       stroke = \"black\",       strokeWidth = 1          # Any other CSS style for the tick     )   ) %>%    GC_legend(y = 10) # Increase space"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"tooltip","dir":"Articles","previous_headings":"","what":"Tooltip","title":"geneviewer","text":"default, tooltip gene chart displays start end positions gene hovering . positions dynamically replaced actual start end data values gene. can customize text tooltip using formatter variable. example , tooltip customized include gene’s start end positions also name. gene name pulled ‘name’ column data set.","code":"GC_chart(ophA_cluster, group = \"class\", height = \"150px\") %>%   GC_tooltip(     formatter = \"Gene: <\/b>{name}
Start:<\/b> {start}
End:<\/b> {end}\",   ) %>%   GC_legend(FALSE)"},{"path":"https://nvelden.github.io/geneviewer/articles/geneviewer.html","id":"saving-plots","dir":"Articles","previous_headings":"","what":"Saving Plots","title":"geneviewer","text":"can save plots directly browser PNG images using save button appears hovering graph. option can disabled setting save_button parameter FALSE GC_chart function. save plots different formats, can use webshot2 package illustrated . plots contain complex elements like gene links, recommended specify width height dimensions explicitly ensure proper rendering.","code":"library(webshot2)  # Generate plot with width and height specifications cluster_plot <-    GC_chart(ophA_clusters,             group = \"class\",             cluster = \"cluster\",            width = \"400px\", # Essential to prevent misalignment of gene links            height = \"250px\")  # Save plot to temp.html file htmlwidgets::saveWidget(cluster_plot, \"temp.html\", selfcontained = TRUE)  # Save plot to .png (or .jpg, .jpeg, .webp, .pdf) webshot2::webshot(   \"temp.html\",    \"output.png\",    zoom = 1, # Increase zoom for higher resolution   selector = \".geneviewer\")"},{"path":"https://nvelden.github.io/geneviewer/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Niels van der Velden. Maintainer.","code":""},{"path":"https://nvelden.github.io/geneviewer/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"van der Velden N (2024). geneviewer: Gene Cluster Visualizations R. R package version 0.1.8, https://github.com/nvelden/geneviewer.","code":"@Manual{,   title = {geneviewer: Gene Cluster Visualizations in R},   author = {Niels {van der Velden}},   year = {2024},   note = {R package version 0.1.8},   url = {https://github.com/nvelden/geneviewer}, }"},{"path":"https://nvelden.github.io/geneviewer/index.html","id":"geneviewer","dir":"","previous_headings":"","what":"geneviewer","title":"Gene Cluster Visualizations in R","text":"geneviewer R package plotting gene clusters transcripts. imports data GenBank, FASTA, GFF files, performs BlastP MUMmer alignments, displays results gene arrow maps. package offers extensive customization options, including legends, labels, annotations, scales, colors, tooltips, . explore features visit package website.","code":""},{"path":"https://nvelden.github.io/geneviewer/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Gene Cluster Visualizations in R","text":"geneviewer still development stage might lead breaking changes thus yet released CRAN. can install development version GitHub :","code":"# install.packages(\"devtools\") devtools::install_github(\"nvelden/geneviewer\")"},{"path":"https://nvelden.github.io/geneviewer/index.html","id":"usage","dir":"","previous_headings":"","what":"Usage","title":"Gene Cluster Visualizations in R","text":"example demonstrates using geneviewer plot gene cluster genomic sequence, using start end positions gene. genes grouped class labels added using GC_labels function.","code":"library(geneviewer)  # Data gene_cluster <- data.frame(   name = c(\"ophB1\", \"ophC\", \"ophA\", \"ophD\", \"ophB2\", \"ophP\", \"ophE\"),   start = c(2522, 5286, 9536, 12616, 13183, 19346, 20170),   end = c(4276, 4718, 10904, 11859, 15046, 16016, 21484),   class = c(\"Monooxygenase\", \"NTF2-like\", \"Methyltransferase\",    \"O-acyltransferase\", \"Monooxygenase\", \"Prolyloligopeptidase\",    \"F-box/RNHI-like\") )  # Chart GC_chart(gene_cluster, group = \"class\", height = \"100px\") %>%   GC_labels(\"name\")"},{"path":"https://nvelden.github.io/geneviewer/index.html","id":"examples","dir":"","previous_headings":"","what":"Examples","title":"Gene Cluster Visualizations in R","text":"additional examples corresponding code create plots, please visit Examples section.","code":""},{"path":"https://nvelden.github.io/geneviewer/index.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Gene Cluster Visualizations in R","text":"encounter issues feature requests, please open Issue.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/BRCA1_splice_variants.html","id":null,"dir":"Reference","previous_headings":"","what":"BRCA1 Splice Variants — BRCA1_splice_variants","title":"BRCA1 Splice Variants — BRCA1_splice_variants","text":"dataset contains detailed information five different splice variants BRCA1 gene. includes data types transcript features (exon, intron, UTR), chromosomal positions, strand orientations, transcript lengths.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/BRCA1_splice_variants.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"BRCA1 Splice Variants — BRCA1_splice_variants","text":"","code":"BRCA1_splice_variants"},{"path":"https://nvelden.github.io/geneviewer/reference/BRCA1_splice_variants.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"BRCA1 Splice Variants — BRCA1_splice_variants","text":"data frame 119 observations 6 variables: ensembl_transcript_id Unique Ensembl transcript identifiers. character vector. type Type transcript feature, indicating whether \"exon\", \"UTR\". character vector. start start position feature chromosome. numeric vector. end end position feature chromosome. numeric vector. strand strand orientation feature, -1 indicating reverse strand. integer vector. transcript_length total length transcript base pairs. integer vector.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/BRCA1_splice_variants.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"BRCA1 Splice Variants — BRCA1_splice_variants","text":"Derived Ensembl website","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_align.html","id":null,"dir":"Reference","previous_headings":"","what":"Align gene clusters — GC_align","title":"Align gene clusters — GC_align","text":"function aligns clusters based specified gene id.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_align.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Align gene clusters — GC_align","text":"","code":"GC_align(GC_chart, id_column, id, align = \"left\")"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_align.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Align gene clusters — GC_align","text":"GC_chart chart object containing genomic data along clustering information. id_column name column contains gene identifiers. id specific identifier gene aligned. align alignment method gene. Valid values \"left\", \"right\", \"center\". Defaults \"left\".","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_align.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Align gene clusters — GC_align","text":"modified `GC_chart` object updated genomic coordinates.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_align.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Align gene clusters — GC_align","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5'),   group = c('A', 'B', 'C', 'C', 'A'),   cluster =  c(1, 1, 1, 2, 2) )   GC_chart(genes_data, group = \"group\", cluster = \"cluster\", height = \"150px\") %>%   GC_align(\"group\", \"A\", align = \"left\") %>%   GC_legend(FALSE)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"150px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"group\":[\"A\",\"B\",\"C\",\"C\",\"A\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"backgroundColor\":\"#0000\"},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90,130],\"end\":[40,120,160],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"B\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":75,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":160,\"start\":-50,\"end\":160},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[170,210],\"end\":[200,240],\"name\":[\"Gene 4\",\"Gene 5\"],\"group\":[\"C\",\"A\"],\"cluster\":[\"2\",\"2\"],\"rowID\":[4,5],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":75,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":170,\"xMax\":240,\"start\":170,\"end\":310},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_annotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Annotations to a GC_chart — GC_annotation","title":"Add Annotations to a GC_chart — GC_annotation","text":"function adds annotations specified clusters within GC chart. Annotations can various types positioned based provided coordinates. types annotations available : text, textMarker, line, arrow, symbol, rectangle, promoter, terminator.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_annotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Annotations to a GC_chart — GC_annotation","text":"","code":"GC_annotation(GC_chart, type = \"textAnnotation\", cluster = NULL, ...)"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_annotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Annotations to a GC_chart — GC_annotation","text":"GC_chart GC chart object annotations added. type Character vector specifying type annotations add. default \"text\". cluster Numeric character vector specifying clusters annotations added. ... Additional parameters customization annotations, depending type.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_annotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Annotations to a GC_chart — GC_annotation","text":"Updated GC chart object added annotations.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/reference/GC_annotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Annotations to a GC_chart — GC_annotation","text":"","code":"genes_data <- data.frame(   start = c(10, 50, 90, 130, 170, 210),   end = c(40, 80, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 1, 2, 2, 2) )  # Adding annotations to a GC chart GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"220px\") %>%   GC_annotation(     type = \"textMarker\",     cluster = 1,     position = 24,     text = \"Gene 1\",     arrowSize = 8   ) %>%   GC_annotation(     type = \"text\",     text = \"feature 1\",     x = 91,     y = 71   ) %>%   GC_annotation(     type = \"symbol\",     symbol = \"triangle\",     x = 95,     y = 64,     size = 10,     rotation = 180   ) %>%   GC_annotation(     type = \"terminator\",     x = 81   ) %>%   GC_annotation(     type = \"promoter\",     x = 49   ) %>%   # Convenience function to track mouse position on hoover   GC_trackMouse()  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"220px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":110,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[{\"type\":\"textMarker\",\"position\":24,\"text\":\"Gene 1\",\"arrowSize\":8},{\"type\":\"text\",\"text\":\"feature 1\",\"x\":91,\"y\":71},{\"type\":\"symbol\",\"symbol\":\"triangle\",\"x\":95,\"y\":64,\"size\":10,\"rotation\":180},{\"type\":\"terminator\",\"x\":81},{\"type\":\"promoter\",\"x\":49}],\"trackMouse\":{\"show\":true},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":110,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[{\"type\":\"text\",\"text\":\"feature 1\",\"x\":91,\"y\":71},{\"type\":\"symbol\",\"symbol\":\"triangle\",\"x\":95,\"y\":64,\"size\":10,\"rotation\":180},{\"type\":\"terminator\",\"x\":81},{\"type\":\"promoter\",\"x\":49}],\"trackMouse\":{\"show\":true},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_chart.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a GC Chart Visualization — GC_chart","title":"Create a GC Chart Visualization — GC_chart","text":"Generates interactive GC chart genomic data.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_chart.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a GC Chart Visualization — GC_chart","text":"","code":"GC_chart(   data,   start = \"start\",   end = \"end\",   cluster = NULL,   group = NULL,   strand = NULL,   width = \"100%\",   height = \"400px\",   style = list(),   elementId = NULL,   save_button = TRUE )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_chart.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a GC Chart Visualization — GC_chart","text":"data Data frame containing genomic information file path folder containing `.gbk` files. providing file path, data loaded processed data frame internally. start Column name indicates start positions. Default \"start\". end Column name indicates end positions. Default \"end\". cluster Optional column name used clustering purposes. Default NULL. group Column name used gene grouping influence color aesthetics. strand Optional column name indicating strand orientation. Acceptable values include 1, 'forward', 'sense', '+' represent forward strand, -1, 0, 'reverse', 'antisense', \"complement\" '-' represent reverse strand. Default NULL, meaning strand information used. width Width specification chart, '100%' 500. Default unspecified. height Height specification chart, '400px' 300. Default unspecified. style list CSS styles applied chart container. element list valid CSS property-value pair. example, list(backgroundColor = \"white\", border = \"2px solid black\"). Default empty list. elementId Optional identifier string widget. Default NULL. save_button Logical, whether include save button. Default TRUE.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_chart.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a GC Chart Visualization — GC_chart","text":"GC chart widget.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_chart.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a GC Chart Visualization — GC_chart","text":"","code":"genes_data <- data.frame(   start = c(10, 50, 90, 130, 170, 210),   end = c(40, 80, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 1, 2, 2, 2) ) # Load from data.frame GC_chart(genes_data, group = \"group\", cluster = \"cluster\", height = \"200px\") %>% GC_labels(\"name\")  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Load from folder containing .gbk files # file_path <- \"~/path/to/folder/\" # GC_chart(file_path) %>%"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_cluster.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify Cluster Settings — GC_cluster","title":"Modify Cluster Settings — GC_cluster","text":"function can switch prevention gene overlap , adjust spacing tracks alter styling specified clusters.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_cluster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify Cluster Settings — GC_cluster","text":"","code":"GC_cluster(   GC_chart,   separate_strands = NULL,   strand_spacing = NULL,   prevent_gene_overlap = NULL,   overlap_spacing = NULL,   cluster = NULL,   style = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_cluster.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify Cluster Settings — GC_cluster","text":"GC_chart gene chart object modified. separate_strands Logical, indicating whether vertically separate forward reverse genes. strand_spacing Numeric, specifies spacing genes different strands. Used `separate_strands` TRUE. prevent_gene_overlap Logical, indicating whether vertically separate overlapping genes. overlap_spacing Numeric, specifies spacing overlapping genes Used `prevent_gene_overlap` TRUE. cluster Optional; used specify clusters chart tooltips. style list CSS styles applied gene track. element list valid CSS property-value pair. example, list(backgroundColor = \"red\", color = \"white\"). ... Additional arguments passed underlying functions.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_cluster.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify Cluster Settings — GC_cluster","text":"Returns modified gene chart object.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_cluster.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Modify Cluster Settings — GC_cluster","text":"","code":"genes_data <- data.frame(   start = c(1, 10, 200, 220, 600),   end = c(10, 150, 180, 400, 400),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5'),   group = c('A', 'A', 'A', 'A', 'A') )   GC_chart(genes_data, group = \"group\", height = \"150px\") %>%   GC_cluster(separate_strands=TRUE, strand_spacing = 0) %>%   GC_legend(FALSE)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"150px\",\"save_button\":true},\"data\":{\"start\":[1,10,200,220,600],\"end\":[10,150,180,400,400],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"group\":[\"A\",\"A\",\"A\",\"A\",\"A\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"reverse\",\"forward\",\"reverse\"]},\"group\":\"group\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"backgroundColor\":\"#0000\"},\"saveButton\":true,\"series\":{\"cluster\":{\"clusterName\":\"cluster\",\"data\":{\"start\":[1,10,200,220,600],\"end\":[10,150,180,400,400],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"group\":[\"A\",\"A\",\"A\",\"A\",\"A\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"reverse\",\"forward\",\"reverse\"],\"cluster\":[\"cluster\",\"cluster\",\"cluster\",\"cluster\",\"cluster\"]},\"cluster\":{\"separateStrands\":true,\"strandSpacing\":0},\"container\":{\"height\":150,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":1,\"xMax\":600},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterFooter.html","id":null,"dir":"Reference","previous_headings":"","what":"Add a Footer to Each Cluster in a GC Chart — GC_clusterFooter","title":"Add a Footer to Each Cluster in a GC Chart — GC_clusterFooter","text":"function allows add footer specific clusters within GC chart. can specify titles, subtitles, control display styling.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterFooter.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add a Footer to Each Cluster in a GC Chart — GC_clusterFooter","text":"","code":"GC_clusterFooter(   GC_chart,   title = NULL,   subtitle = NULL,   height = NULL,   show = TRUE,   cluster = NULL,   subtitleFont = list(),   titleFont = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterFooter.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add a Footer to Each Cluster in a GC Chart — GC_clusterFooter","text":"GC_chart GC chart object footers added . title Character vector NULL. title displayed footer. Multiple titles can provided different clusters, recycled clusters titles. Default NULL. subtitle Character vector NULL. Subtitles accompany main titles. Default NULL. height Character vector NULL. height footer, can vary clusters. Default NULL. show Logical vector. Controls visibility footer. Default TRUE clusters. cluster Numeric character vector specifying clusters footers added updated. NULL, clusters updated. Default NULL. subtitleFont List, styling options subtitle. titleFont List, styling options title. ... Additional arguments customization footers.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterFooter.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add a Footer to Each Cluster in a GC Chart — GC_clusterFooter","text":"GC chart object updated footer settings specified cluster.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterFooter.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add a Footer to Each Cluster in a GC Chart — GC_clusterFooter","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 2, 2, 2) )  # Add a simple footer with subtitle to all clusters GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"300px\") %>%   GC_clusterFooter(     title = \"Cluster Footer\",     subtitle = \"Cluster subtitle\"   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"300px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":150,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":{\"title\":\"Cluster Footer\",\"subtitle\":\"Cluster subtitle\",\"show\":true,\"subtitleFont\":[],\"titleFont\":[]},\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"},\"grid\":{\"bottom\":\"20px\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":150,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":{\"title\":\"Cluster Footer\",\"subtitle\":\"Cluster subtitle\",\"show\":true,\"subtitleFont\":[],\"titleFont\":[]},\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"},\"grid\":{\"bottom\":\"20px\"}}}},\"evals\":[],\"jsHooks\":[]}# Add styling to the title and sub title GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"300px\") %>%   GC_clusterFooter(     title = \"This is a footer\",     subtitle = \"Subtitle for the footer\",     height = \"15px\",     spacing = 15,     show = TRUE,     cluster = 1,     x = 6,     y = -20,     align = \"center\", # left / right     spacing = 12,     titleFont = list(       fontSize = \"12px\",       fontWeight = \"bold\",       fontFamily = \"sans-serif\",       fill = \"black\",       cursor = \"default\"     ),     subtitleFont = list(       fill = \"grey\",       fontSize = \"10px\",       fontStyle = \"normal\",       fontFamily = \"sans-serif\",       cursor = \"default\"     )   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"300px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":150,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":{\"title\":\"This is a footer\",\"subtitle\":\"Subtitle for the footer\",\"show\":true,\"subtitleFont\":{\"fill\":\"grey\",\"fontSize\":\"10px\",\"fontStyle\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\"},\"titleFont\":{\"fontSize\":\"12px\",\"fontWeight\":\"bold\",\"fontFamily\":\"sans-serif\",\"fill\":\"black\",\"cursor\":\"default\"},\"spacing\":15,\"x\":6,\"y\":-20,\"align\":\"center\"},\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"},\"grid\":{\"bottom\":\"15px\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":150,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterLabel.html","id":null,"dir":"Reference","previous_headings":"","what":"Set or Update Cluster Labels for a GC Chart — GC_clusterLabel","title":"Set or Update Cluster Labels for a GC Chart — GC_clusterLabel","text":"function allows set update labels specified clusters within GC chart. provides flexibility terms title, visibility, width, position, additional customization options.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterLabel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set or Update Cluster Labels for a GC Chart — GC_clusterLabel","text":"","code":"GC_clusterLabel(   GC_chart,   title = NULL,   show = TRUE,   width = \"100px\",   cluster = NULL,   position = \"left\",   wrapLabel = TRUE,   wrapOptions = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterLabel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set or Update Cluster Labels for a GC Chart — GC_clusterLabel","text":"GC_chart GC chart object. title Character vector. title cluster label. Default NULL. show Logical. Whether show cluster label. Default TRUE. width Character. width cluster label. Default \"100px\". cluster Numeric character vector. Clusters GC chart update. Default NULL. position Character. Position label, either \"left\" \"right\". Default \"left\". wrapLabel Logical. Indicates whether label wrapped. Default TRUE. wrapOptions List. Specifies wrapping options. Default empty List. ... Additional customization arguments cluster label, 'fontSize', 'fontStyle', 'fontWeight', 'fontFamily', 'cursor', etc.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterLabel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set or Update Cluster Labels for a GC Chart — GC_clusterLabel","text":"Updated GC chart new modified cluster labels.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterLabel.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set or Update Cluster Labels for a GC Chart — GC_clusterLabel","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 2, 2, 2) )  # Set cluster labels GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"200px\") %>% GC_clusterLabel(title = unique(genes_data$cluster))  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"},\"margin\":{\"left\":\"100px\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":1,\"show\":true,\"wrapLabel\":true,\"wrapOptions\":[],\"position\":\"left\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":2,\"show\":true,\"wrapLabel\":true,\"wrapOptions\":[],\"position\":\"left\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Set label for a specific cluster GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"200px\") %>% GC_clusterLabel(title = \"Cluster 1\", cluster = 1)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"},\"margin\":{\"left\":\"100px\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":\"Cluster 1\",\"show\":true,\"wrapLabel\":true,\"wrapOptions\":[],\"position\":\"left\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Style labels GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"200px\") %>%   GC_clusterLabel(     title = c(\"Cluster 1\", \"Cluster 2\"),     width = \"100px\",     x = 0,     y = 0,     position = \"left\",     wrapLabel = TRUE,     wrapOptions = list(       dyAdjust = 0,       lineHeightEms = 1.05,       lineHeightSquishFactor =  1,       splitOnHyphen =  TRUE,       centreVertically = TRUE      ),     fontSize = \"12px\",     fontStyle = \"normal\",     fontWeight = \"bold\",     fontFamily = \"sans-serif\",     cursor = \"default\"   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"},\"margin\":{\"left\":\"100px\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":\"Cluster 1\",\"show\":true,\"wrapLabel\":true,\"wrapOptions\":{\"dyAdjust\":0,\"lineHeightEms\":1.05,\"lineHeightSquishFactor\":1,\"splitOnHyphen\":true,\"centreVertically\":true},\"position\":\"left\",\"x\":0,\"y\":0,\"fontSize\":\"12px\",\"fontStyle\":\"normal\",\"fontWeight\":\"bold\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":\"Cluster 2\",\"show\":true,\"wrapLabel\":true,\"wrapOptions\":{\"dyAdjust\":0,\"lineHeightEms\":1.05,\"lineHeightSquishFactor\":1,\"splitOnHyphen\":true,\"centreVertically\":true},\"position\":\"left\",\"x\":0,\"y\":0,\"fontSize\":\"12px\",\"fontStyle\":\"normal\",\"fontWeight\":\"bold\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterTitle.html","id":null,"dir":"Reference","previous_headings":"","what":"Update cluster Title of a GC Chart Cluster — GC_clusterTitle","title":"Update cluster Title of a GC Chart Cluster — GC_clusterTitle","text":"Modify cluster title subtitle specified clusters within GC chart adjust display settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterTitle.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update cluster Title of a GC Chart Cluster — GC_clusterTitle","text":"","code":"GC_clusterTitle(   GC_chart,   title = NULL,   subtitle = NULL,   subtitleFont = list(),   titleFont = list(),   show = TRUE,   height = NULL,   cluster = NULL,   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterTitle.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update cluster Title of a GC Chart Cluster — GC_clusterTitle","text":"GC_chart GC chart object. title Character vector. Titles set clusters. subtitle Character vector. Subtitles set clusters. subtitleFont List. Settings subtitle font. titleFont List. Settings title font. show Logical. Whether display title. Default TRUE. height Character. Height title (e.g., \"40px\"). cluster Numeric character vector. Clusters GC chart update. ... Additional customization arguments title subtitle.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterTitle.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update cluster Title of a GC Chart Cluster — GC_clusterTitle","text":"Updated GC chart new title settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_clusterTitle.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update cluster Title of a GC Chart Cluster — GC_clusterTitle","text":"","code":"genes_data <- data.frame(   start = c(10, 50, 90, 130, 170, 210),   end = c(40, 80, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 1, 2, 2, 2) )  # Basic usage GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"400px\") %>% GC_labels(\"name\") %>% GC_clusterTitle(   title = \"Cluster 1 Data\",   subtitle = \"Detailed View\",   show = TRUE,   cluster = 1 )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"400px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":{\"title\":\"Cluster 1 Data\",\"subtitle\":\"Detailed View\",\"subtitleFont\":[],\"titleFont\":[],\"show\":true},\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Customizing title style GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"400px\") %>%   GC_labels(\"name\") %>%   GC_clusterTitle(     title = \"Cluster 1 Data\",     subtitle = \"Detailed View\",     show = TRUE,     cluster = 1,     x = 0,     y = 5,     align = \"center\",     spacing = 20,     titleFont = list(       fontSize = \"16px\",       fontStyle = \"normal\",       fontWeight = \"bold\",       textDecoration = \"normal\",       fontFamily = \"sans-serif\",       cursor = \"default\",       fill = \"black\"       # Any other CSS styles     ),     subtitleFont = list(       fontSize = \"14px\",       fontStyle = \"normal\",       fontWeight = \"bold\",       textDecoration = \"normal\",       fontFamily = \"sans-serif\",       cursor = \"default\",       fill = \"black\"       # Any other CSS styles     )   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"400px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":{\"title\":\"Cluster 1 Data\",\"subtitle\":\"Detailed View\",\"subtitleFont\":{\"fontSize\":\"14px\",\"fontStyle\":\"normal\",\"fontWeight\":\"bold\",\"textDecoration\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"fill\":\"black\"},\"titleFont\":{\"fontSize\":\"16px\",\"fontStyle\":\"normal\",\"fontWeight\":\"bold\",\"textDecoration\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"fill\":\"black\"},\"show\":true,\"x\":0,\"y\":5,\"align\":\"center\",\"spacing\":20},\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_color.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Color Scheme in Gene Chart — GC_color","title":"Update Color Scheme in Gene Chart — GC_color","text":"function updates color scheme legend genes gene chart.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_color.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Color Scheme in Gene Chart — GC_color","text":"","code":"GC_color(GC_chart, colorScheme = NULL, customColors = NULL)"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_color.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Color Scheme in Gene Chart — GC_color","text":"GC_chart gene chart object modified. colorScheme Optional; character NULL, name predefined color scheme apply genes.Acceptable values include D3.js's built-color schemes like \"schemeCategory10\", \"schemeAccent\", \"schemeTableau10\". customColors Either NULL, list color values, named list color values.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_color.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Color Scheme in Gene Chart — GC_color","text":"Returns gene chart object updated color settings genes.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_color.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update Color Scheme in Gene Chart — GC_color","text":"","code":"genes_data <- data.frame(   start = c(10, 50, 90, 130, 170, 210),   end = c(40, 80, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 1, 2, 2, 2) )  GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"100px\") %>%   GC_color(colorScheme = \"schemeCategory10\")  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"100px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"legendOptions\":{\"colorScheme\":\"schemeCategory10\"}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":50,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true,\"colorScheme\":\"schemeCategory10\"},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false,\"colorScheme\":\"schemeCategory10\"},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":50,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true,\"colorScheme\":\"schemeCategory10\"},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false,\"colorScheme\":\"schemeCategory10\"},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"100px\") %>%   GC_color(customColors = c(\"red\", \"orange\", \"green\"))  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"100px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"legendOptions\":{\"customColors\":[\"red\",\"orange\",\"green\"]}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":50,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true,\"customColors\":[\"red\",\"orange\",\"green\"]},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false,\"customColors\":[\"red\",\"orange\",\"green\"]},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":50,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true,\"customColors\":[\"red\",\"orange\",\"green\"]},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false,\"customColors\":[\"red\",\"orange\",\"green\"]},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"100px\") %>%   GC_color(customColors = list(A = \"yellow\", B = \"pink\", C =  \"purple\"))  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"100px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"legendOptions\":{\"customColors\":{\"A\":\"yellow\",\"B\":\"pink\",\"C\":\"purple\"}}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":50,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true,\"customColors\":{\"A\":\"yellow\",\"B\":\"pink\",\"C\":\"purple\"}},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false,\"customColors\":{\"A\":\"yellow\",\"B\":\"pink\",\"C\":\"purple\"}},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":50,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true,\"customColors\":{\"A\":\"yellow\",\"B\":\"pink\",\"C\":\"purple\"}},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false,\"customColors\":{\"A\":\"yellow\",\"B\":\"pink\",\"C\":\"purple\"}},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_coordinates.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify Coordinates in a GC Chart — GC_coordinates","title":"Modify Coordinates in a GC Chart — GC_coordinates","text":"function updates GC chart modifying coordinates settings. allows showing hiding tick values, applying custom tick values top bottom axes, supports several customizations specific clusters chart.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_coordinates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify Coordinates in a GC Chart — GC_coordinates","text":"","code":"GC_coordinates(   GC_chart,   show = TRUE,   tickValuesTop = NULL,   tickValuesBottom = NULL,   ticksFormat = NULL,   tickStyle = list(),   textStyle = list(),   cluster = NULL,   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_coordinates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify Coordinates in a GC Chart — GC_coordinates","text":"GC_chart GC chart object modified. show Logical, whether show tick values . Can single value vector. tickValuesTop Numeric vector NULL, custom tick values used top cluster. NULL, default tick values used. tickValuesBottom Numeric vector NULL, custom tick values used bottom cluster. NULL, default tick values used. ticksFormat Format tick labels. Default \",.0f\". tickStyle List, styling options ticks. textStyle List, styling options text. coordinate modifications. NULL, applies clusters. cluster Numeric character vector NULL; specifies clusters generate coordinates .        NULL, labels applied clusters. Default NULL. ... Additional arguments passed coordinate options.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_coordinates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify Coordinates in a GC Chart — GC_coordinates","text":"Returns GC chart object updated coordinates.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_coordinates.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Modify Coordinates in a GC Chart — GC_coordinates","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5'),   cluster = c(1, 1, 2, 2, 2) )  # Add coordinates to all clusters GC_chart(genes_data, cluster = \"cluster\", group = \"name\", height = \"200px\") %>% GC_coordinates()  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"name\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"name\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"name\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 2\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"name\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"name\",\"show\":false},\"labels\":{\"group\":\"name\",\"show\":true},\"coordinates\":{\"show\":true,\"ticksFormat\":null,\"tickStyle\":[],\"textStyle\":[]},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"name\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"name\",\"show\":false},\"labels\":{\"group\":\"name\",\"show\":true},\"coordinates\":{\"show\":true,\"ticksFormat\":null,\"tickStyle\":[],\"textStyle\":[]},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Modify coordinates of a specific cluster GC_chart(genes_data, cluster = \"cluster\", group = \"name\", height = \"200px\") %>% GC_coordinates() %>% GC_coordinates(   cluster = 2,   show = TRUE,   tickValuesTop = c(130, 170, 210, 240),   tickValuesBottom = c(160, 200),   ticksFormat = \",.0f\", # \".2s\",   rotate = -45,   yPositionTop = 55,   yPositionBottom = 45,   overlapThreshold = 20,   tickStyle = list(   stroke = \"black\",   strokeWidth = 1,   lineLength = 6   ),   textStyle = list(   fill = \"black\",   fontSize = \"12px\",   fontFamily = \"Arial\",   cursor = \"default\"   ) )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"name\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"name\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"name\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 2\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"name\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"name\",\"show\":false},\"labels\":{\"group\":\"name\",\"show\":true},\"coordinates\":{\"show\":true,\"ticksFormat\":null,\"tickStyle\":[],\"textStyle\":[]},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"name\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"name\",\"show\":false},\"labels\":{\"group\":\"name\",\"show\":true},\"coordinates\":{\"show\":true,\"ticksFormat\":\",.0f\",\"tickStyle\":{\"stroke\":\"black\",\"strokeWidth\":1,\"lineLength\":6},\"textStyle\":{\"fill\":\"black\",\"fontSize\":\"12px\",\"fontFamily\":\"Arial\",\"cursor\":\"default\"},\"rotate\":-45,\"yPositionTop\":55,\"yPositionBottom\":45,\"overlapThreshold\":20,\"tickValuesTop\":[130,170,210,240],\"tickValuesBottom\":[160,200]},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify Gene Characteristics within a Chart — GC_genes","title":"Modify Gene Characteristics within a Chart — GC_genes","text":"function updates gene chart specific characteristics genes based given parameters. can show/hide genes, apply color scheme, assign custom colors, filter cluster, accept additional options.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify Gene Characteristics within a Chart — GC_genes","text":"","code":"GC_genes(   GC_chart,   group = NULL,   marker = NULL,   marker_size = NULL,   show = TRUE,   colorScheme = NULL,   customColors = NULL,   cluster = NULL,   itemStyle = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify Gene Characteristics within a Chart — GC_genes","text":"GC_chart gene chart object modified. group Column name used gene grouping influence color aesthetics. marker Character NULL, type marker represent genes chart. Allowed values 'arrow', 'boxarrow', 'box', 'cbox', 'rbox'. marker_size Character NULL, size category marker ('small', 'medium', 'large'). show Logical, whether show genes . colorScheme Character NULL, name color scheme use. customColors List NULL, custom colors apply genes. cluster Numeric character, specific cluster filter genes . itemStyle List, list styles apply individual items chart. ... Additional arguments passed gene options.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify Gene Characteristics within a Chart — GC_genes","text":"Returns modified gene chart object.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Modify Gene Characteristics within a Chart — GC_genes","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 2, 2, 2) )  # Change the appearance of a specific gene cluster GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"200px\") %>%   GC_genes(     group = \"group\",     show = TRUE,     marker = \"arrow\",     marker_size = \"medium\",     colorScheme = NULL, # One of D3.js build in colorSchemes                         # (eg. \"schemeCategory10\",                         # \"schemeAccent\", \"schemeTableau10\")     customColors = NULL, # A vector of color names     prevent_overlap = FALSE,     gene_overlap_spacing = 40,     cluster = 1, # Specify a specific cluster     x = 1,     y = 50,     stroke = \"black\",     strokeWidth = 1,     arrowheadWidth = NULL,     arrowheadHeight = NULL,     arrowHeight = NULL,     markerHeight = NULL # overwrites marker_size    )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"marker\":\"arrow\",\"markerSize\":\"medium\",\"show\":true,\"prevent_overlap\":false,\"gene_overlap_spacing\":40,\"x\":1,\"y\":50,\"stroke\":\"black\",\"strokeWidth\":1},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Change the appearance of a specific gene GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"200px\") %>% GC_genes(   cluster = 2,   itemStyle = list(list(index = 2, fill = \"red\", stroke = \"blue\")   )  )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true,\"itemStyle\":[{\"index\":2,\"fill\":\"red\",\"stroke\":\"blue\"}]},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_grid.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Grid Display of a GC Chart Cluster — GC_grid","title":"Update Grid Display of a GC Chart Cluster — GC_grid","text":"Modify grid display specified clusters within GC chart. function allows users adjust margins, width, height grid cluster.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_grid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Grid Display of a GC Chart Cluster — GC_grid","text":"","code":"GC_grid(   GC_chart,   margin = NULL,   width = NULL,   height = NULL,   direction = \"column\",   cluster = NULL )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_grid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Grid Display of a GC Chart Cluster — GC_grid","text":"GC_chart GC chart object. margin list specifying top, right, bottom, left margins. width Numeric character. Width grid. numeric, considered percentage. height Numeric. Height grid. direction Character. Layout direction grid, either \"column\" (default) vertical \"row\" horizontal. cluster Numeric character vector. Clusters GC chart update.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_grid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Grid Display of a GC Chart Cluster — GC_grid","text":"Updated GC chart new grid display settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_grid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update Grid Display of a GC Chart Cluster — GC_grid","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 2, 2, 2) )  # Set Margin of clusters GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"200px\") %>% GC_grid(margin = list(left = \"50px\", right = \"0px\"))  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"},\"margin\":{\"left\":\"50px\",\"right\":\"0px\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"50px\",\"right\":\"0px\"}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"50px\",\"right\":\"0px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"50px\",\"right\":\"0px\"}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Set height of a specific cluster GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"200px\") %>% GC_grid(height = \"120px\", cluster = 2)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":120,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Labels to Each Cluster in a GC Chart — GC_labels","title":"Add Labels to Each Cluster in a GC Chart — GC_labels","text":"function adds labels cluster within GC chart. provides option show hide labels supports customization label properties. can automatically pick group names labels `GC_chart` object provided.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Labels to Each Cluster in a GC Chart — GC_labels","text":"","code":"GC_labels(   GC_chart,   label = NULL,   show = TRUE,   cluster = NULL,   itemStyle = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Labels to Each Cluster in a GC Chart — GC_labels","text":"GC_chart `GC chart` object labels added. label Character vector, logical, NULL. Specific labels clusters. NULL `GC_chart` group names, used labels. show Logical; controls visibility labels. Default `TRUE`. cluster Numeric character vector NULL; specifies clusters labeled. NULL, labels applied clusters. Default NULL. itemStyle List, list styles apply individual items chart. ... Additional arguments customization labels.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Labels to Each Cluster in a GC Chart — GC_labels","text":"`GC chart` object updated label settings specified cluster.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Labels to Each Cluster in a GC Chart — GC_labels","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 2, 2, 2) )  # Add labels to all clusters GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"200px\") %>% GC_labels()  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Add labels and styling GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"200px\") %>% GC_labels(  label = \"group\",  show = TRUE,  x = 0,  y = 50,  dy = \"-1.2em\",  dx = \"0em\",  rotate = 0,  adjustLabels = TRUE, # Rotate labels to prevent overlap  fontSize = \"12px\",  fontStyle = \"italic\",  fill = \"black\",  fontFamily = \"sans-serif\",  textAnchor = \"middle\",  cursor = \"default\", )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"group\",\"x\":0,\"y\":50,\"dy\":\"-1.2em\",\"dx\":\"0em\",\"rotate\":0,\"adjustLabels\":true,\"fontSize\":\"12px\",\"fontStyle\":\"italic\",\"fill\":\"black\",\"fontFamily\":\"sans-serif\",\"textAnchor\":\"middle\",\"cursor\":\"default\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"group\",\"x\":0,\"y\":50,\"dy\":\"-1.2em\",\"dx\":\"0em\",\"rotate\":0,\"adjustLabels\":true,\"fontSize\":\"12px\",\"fontStyle\":\"italic\",\"fill\":\"black\",\"fontFamily\":\"sans-serif\",\"textAnchor\":\"middle\",\"cursor\":\"default\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Alter style of a specific label GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"200px\") %>% GC_labels(label = \"group\") %>% GC_labels(   cluster = 1,   itemStyle = list(     list(index = 0, fill = \"red\", fontSize = \"14px\", fontWeight = \"bold\")   ) )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"group\",\"itemStyle\":[{\"index\":0,\"fill\":\"red\",\"fontSize\":\"14px\",\"fontWeight\":\"bold\"}]},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_legend.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Legend for a Gene Chart — GC_legend","title":"Set Legend for a Gene Chart — GC_legend","text":"function configures legend gene chart. allows toggling legend's visibility, setting background color, assigning custom labels legend entries. function can also handle additional customizations various options.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_legend.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Legend for a Gene Chart — GC_legend","text":"","code":"GC_legend(   GC_chart,   group = NULL,   show = TRUE,   backgroundColor = \"#0000\",   order = list(),   position = \"bottom\",   style = list(),   legendOptions = list(),   legendTextOptions = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_legend.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Legend for a Gene Chart — GC_legend","text":"GC_chart gene chart object modified. group Optional; character NULL, specifies groups include legend. NULL, groups taken 'group' attribute 'GC_chart' object. show Logical, specifies whether display legend. backgroundColor String, background color legend. order Optional; list, specifies order legend labels. position Character. Position legend, either \"top\" \"bottom\". Default \"bottom\". style list CSS styles applied chart container. element list valid CSS property-value pair. example, list(backgroundColor = \"white\", border = \"2px solid black\"). Default empty list. legendOptions List, additional options legend. legendTextOptions List, additional text options legend. ... Additional arguments passed legend configuration.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_legend.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Legend for a Gene Chart — GC_legend","text":"Returns modified gene chart object legend configured.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_legend.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set Legend for a Gene Chart — GC_legend","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'B', 'B', 'A', 'C'),   cluster = c('A', 'A', 'A', 'B', 'B') )  # Customize legend GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"200px\") %>%   GC_legend(     position = \"top\", #bottom     orientation = \"horizontal\", #vertical     x = 0,     y = 0,     width = NULL, # 100 / \"100px\" / 50%     adjustHeight = TRUE,     backgroundColor = \"#0000\",     order = list(),     positions = \"bottom\",     style = list(       backgroundColor = \"#0000\"       # Any other CSS styles     ),     legendOptions = list(       cursor = \"pointer\",       colorScheme = NULL,       customColors = NULL # c(\"red\", \"green\", \"orange\")       # Additional styles     ),     legendTextOptions = list(       cursor = \"pointer\",       textAnchor = \"start\",       dy = \".35em\",       fontSize = \"12px\",       fontFamily = \"sans-serif\",       fill = \"black\"       # Additional styles     )   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"A\",\"A\",\"A\",\"B\",\"B\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"top\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":\"#0000\"},\"backgroundColor\":\"#0000\",\"legendOptions\":{\"cursor\":\"pointer\",\"colorScheme\":null,\"customColors\":null},\"legendTextOptions\":{\"cursor\":\"pointer\",\"textAnchor\":\"start\",\"dy\":\".35em\",\"fontSize\":\"12px\",\"fontFamily\":\"sans-serif\",\"fill\":\"black\"},\"orientation\":\"horizontal\",\"x\":0,\"y\":0,\"adjustHeight\":true,\"positions\":\"bottom\"},\"saveButton\":true,\"series\":{\"A\":{\"clusterName\":\"A\",\"data\":{\"start\":[10,90,130],\"end\":[40,120,160],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\"],\"group\":[\"A\",\"B\",\"B\"],\"cluster\":[\"A\",\"A\",\"A\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":160},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"B\":{\"clusterName\":\"B\",\"data\":{\"start\":[170,210],\"end\":[200,240],\"name\":[\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"C\"],\"cluster\":[\"B\",\"B\"],\"rowID\":[4,5],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":170,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_links.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Links to GC Chart — GC_links","title":"Add Links to GC Chart — GC_links","text":"Add links generated `get_links` `GC_chart` object. Links added graph respective rowIDs.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_links.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Links to GC Chart — GC_links","text":"","code":"GC_links(   GC_chart,   group = NULL,   data = NULL,   value1 = NULL,   value2 = NULL,   cluster = NULL,   curve = TRUE,   measure = \"identity\",   show_links = TRUE,   label = TRUE,   normal_color = \"#969696\",   inverted_color = \"#d62728\",   use_group_colors = FALSE,   color_bar = TRUE,   colorBarOptions = list(),   linkStyle = list(),   labelStyle = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_links.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Links to GC Chart — GC_links","text":"GC_chart Gene chart object. group name column data create value pairs . data data.frame containing linking data. value1 Optional vector group values generate links . value2 Optional vector group values generate links . cluster Numeric character vector NULL; specifies clusters. curve Logical; `TRUE`, links curved, otherwise straight. measure Character; specifies measure use link color intensity. \"identity\", \"similarity\", \"none\". show_links Logical; `TRUE`, links shown, otherwise hidden. label Logical; `TRUE`, shows measure labels links, otherwise hidden. normal_color Color links normal state. inverted_color Color inverted links. use_group_colors Logical; `TRUE`, color links group. color_bar Logical; `TRUE`, color bar displayed. colorBarOptions List options customize color bar appearance. linkStyle list CSS styles apply links. labelStyle list CSS styles specifically labels. ... Additional arguments passed links.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_links.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Links to GC Chart — GC_links","text":"Modified `GC_chart` object added links.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/reference/GC_links.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Links to GC Chart — GC_links","text":"","code":"# Add links between all groups in each cluster genes_data <- data.frame(   start = c(10, 90, 130, 170, 240, 250, 300, 340, 380, 420),   end = c(40, 120, 160, 200, 210, 270, 330, 370, 410, 450),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5',            'Gene 6', 'Gene 7', 'Gene 8', 'Gene 9', 'Gene 10'),   group = c('A', 'B', 'C', 'A', 'B', 'C', 'A', 'B', 'C', 'D'),   identity = c(NA, NA, NA, 50, 40, 100, 60, 65, 20, NA),   similarity = c(NA, NA, NA, 40, 30, 90, 50, 55, 10, NA),   cluster = c(1, 1, 1, 2, 2, 2, 3, 3, 3, 3) ) GC_chart(genes_data,          cluster = \"cluster\",          height = \"200px\") %>%   GC_links(     group = \"group\",     value1 = \"A\",     value2 = \"B\",     measure = \"identity\",     label = FALSE) %>%   GC_labels(label = \"group\")  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,240,250,300,340,380,420],\"end\":[40,120,160,200,210,270,330,370,410,450],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\",\"Gene 7\",\"Gene 8\",\"Gene 9\",\"Gene 10\"],\"group\":[\"A\",\"B\",\"C\",\"A\",\"B\",\"C\",\"A\",\"B\",\"C\",\"D\"],\"identity\":[null,null,null,50,40,100,60,65,20,null],\"similarity\":[null,null,null,40,30,90,50,55,10,null],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\",\"3\",\"3\",\"3\",\"3\"],\"rowID\":[1,2,3,4,5,6,7,8,9,10],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"reverse\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":null,\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90,130],\"end\":[40,120,160],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"B\",\"C\"],\"identity\":[null,null,null],\"similarity\":[null,null,null],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":160},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[170,240,250],\"end\":[200,210,270],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"C\"],\"identity\":[50,40,100],\"similarity\":[40,30,90],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"reverse\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":170,\"xMax\":270},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"3\":{\"clusterName\":\"3\",\"data\":{\"start\":[300,340,380,420],\"end\":[330,370,410,450],\"name\":[\"Gene 7\",\"Gene 8\",\"Gene 9\",\"Gene 10\"],\"group\":[\"A\",\"B\",\"C\",\"D\"],\"identity\":[60,65,20,null],\"similarity\":[50,55,10,null],\"cluster\":[\"3\",\"3\",\"3\",\"3\"],\"rowID\":[7,8,9,10],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":300,\"xMax\":450},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}},\"links\":[{\"data\":{\"cluster1\":[\"1\",\"2\"],\"group1\":[\"A\",\"A\"],\"start1\":[10,170],\"end1\":[40,200],\"cluster2\":[\"2\",\"3\"],\"group2\":[\"B\",\"B\"],\"start2\":[240,340],\"end2\":[210,370],\"identity\":[40,65],\"linkID\":[\"0-1\",\"0-2\"]},\"options\":{\"group\":\"group\",\"curve\":true,\"measure\":\"identity\",\"showLinks\":true,\"label\":false,\"normalColor\":\"#969696\",\"invertedColor\":\"#d62728\",\"useGroupColors\":false,\"value1\":\"A\",\"value2\":\"B\",\"colorBar\":true}}]},\"evals\":[],\"jsHooks\":[]} # Add links between group A of cluster 1 and A and B of cluster 2 GC_chart(genes_data,          cluster = \"cluster\",          height = \"200px\") %>%          GC_labels(label = \"group\") %>%          GC_links(group = \"group\",                    value1 = c(\"A\", \"A\"),                    value2 = c(\"B\", \"A\"),                    label = FALSE,                    cluster = c(1,2))  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,240,250,300,340,380,420],\"end\":[40,120,160,200,210,270,330,370,410,450],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\",\"Gene 7\",\"Gene 8\",\"Gene 9\",\"Gene 10\"],\"group\":[\"A\",\"B\",\"C\",\"A\",\"B\",\"C\",\"A\",\"B\",\"C\",\"D\"],\"identity\":[null,null,null,50,40,100,60,65,20,null],\"similarity\":[null,null,null,40,30,90,50,55,10,null],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\",\"3\",\"3\",\"3\",\"3\"],\"rowID\":[1,2,3,4,5,6,7,8,9,10],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"reverse\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":null,\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90,130],\"end\":[40,120,160],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"B\",\"C\"],\"identity\":[null,null,null],\"similarity\":[null,null,null],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":160},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[170,240,250],\"end\":[200,210,270],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"C\"],\"identity\":[50,40,100],\"similarity\":[40,30,90],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"reverse\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":170,\"xMax\":270},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"3\":{\"clusterName\":\"3\",\"data\":{\"start\":[300,340,380,420],\"end\":[330,370,410,450],\"name\":[\"Gene 7\",\"Gene 8\",\"Gene 9\",\"Gene 10\"],\"group\":[\"A\",\"B\",\"C\",\"D\"],\"identity\":[60,65,20,null],\"similarity\":[50,55,10,null],\"cluster\":[\"3\",\"3\",\"3\",\"3\"],\"rowID\":[7,8,9,10],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":300,\"xMax\":450},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}},\"links\":[{\"data\":{\"cluster1\":[\"1\",\"1\"],\"group1\":[\"A\",\"A\"],\"start1\":[10,10],\"end1\":[40,40],\"cluster2\":[\"2\",\"2\"],\"group2\":[\"A\",\"B\"],\"start2\":[170,240],\"end2\":[200,210],\"identity\":[50,40],\"linkID\":[\"0-1\",\"0-2\"]},\"options\":{\"group\":\"group\",\"curve\":true,\"measure\":\"identity\",\"showLinks\":true,\"label\":false,\"normalColor\":\"#969696\",\"invertedColor\":\"#d62728\",\"useGroupColors\":false,\"value1\":[\"A\",\"A\"],\"value2\":[\"B\",\"A\"],\"colorBar\":true}}]},\"evals\":[],\"jsHooks\":[]} # Style links and color bar GC_chart(genes_data,          cluster = \"cluster\",          height = \"200px\" ) %>%   GC_links(     group = \"group\",     data = NULL,     curve = TRUE,     measure = \"identity\",     show_links = TRUE,     label = TRUE,     normal_color = \"#1f77b4\",     inverted_color = \"#d62728\",     use_group_colors = FALSE,     color_bar = TRUE,     colorBarOptions = list(       x = 0,       y = 24,       width = 10,       height = 60,       labelOptions = list(         fontSize = 8,         xOffset = 2,         yOffset = 0         # Any other CSS style       ),       titleOptions = list(         fontSize = 10,         xOffset = 2,         yOffset = 0         # Any other CSS style       ),       barOptions = list(         stroke = \"#000\",         strokeWidth = 0.5,         opacity = 1         # Any other CSS style       )     ),     linkStyle = list(       stroke = \"black\",       strokeWidth = 0.5,       fillOpacity = 0.4       # Any other CSS style     ),     labelStyle = list(       fontSize = \"8px\"       # Any other CSS style     )   ) %>%   GC_labels(label = \"group\", cluster = 1) %>%   GC_clusterLabel()  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,240,250,300,340,380,420],\"end\":[40,120,160,200,210,270,330,370,410,450],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\",\"Gene 7\",\"Gene 8\",\"Gene 9\",\"Gene 10\"],\"group\":[\"A\",\"B\",\"C\",\"A\",\"B\",\"C\",\"A\",\"B\",\"C\",\"D\"],\"identity\":[null,null,null,50,40,100,60,65,20,null],\"similarity\":[null,null,null,40,30,90,50,55,10,null],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\",\"3\",\"3\",\"3\",\"3\"],\"rowID\":[1,2,3,4,5,6,7,8,9,10],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"reverse\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"},\"margin\":{\"left\":\"100px\"}},\"legend\":{\"group\":null,\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90,130],\"end\":[40,120,160],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"B\",\"C\"],\"identity\":[null,null,null],\"similarity\":[null,null,null],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":160},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true,\"label\":\"group\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":\"1\",\"show\":true,\"wrapLabel\":true,\"wrapOptions\":[],\"position\":\"left\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[170,240,250],\"end\":[200,210,270],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"C\"],\"identity\":[50,40,100],\"similarity\":[40,30,90],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"reverse\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":170,\"xMax\":270},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":\"2\",\"show\":true,\"wrapLabel\":true,\"wrapOptions\":[],\"position\":\"left\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"3\":{\"clusterName\":\"3\",\"data\":{\"start\":[300,340,380,420],\"end\":[330,370,410,450],\"name\":[\"Gene 7\",\"Gene 8\",\"Gene 9\",\"Gene 10\"],\"group\":[\"A\",\"B\",\"C\",\"D\"],\"identity\":[60,65,20,null],\"similarity\":[50,55,10,null],\"cluster\":[\"3\",\"3\",\"3\",\"3\"],\"rowID\":[7,8,9,10],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":66.66666666666667,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"margin\":{\"left\":\"100px\"}},\"genes\":{\"group\":null,\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":300,\"xMax\":450},\"transcript\":{\"group\":null,\"show\":false},\"labels\":{\"group\":null,\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":{\"title\":\"3\",\"show\":true,\"wrapLabel\":true,\"wrapOptions\":[],\"position\":\"left\"},\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}},\"links\":[{\"data\":{\"cluster1\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"group1\":[\"A\",\"B\",\"C\",\"A\",\"B\",\"C\"],\"start1\":[10,90,130,170,240,250],\"end1\":[40,120,160,200,210,270],\"cluster2\":[\"2\",\"2\",\"2\",\"3\",\"3\",\"3\"],\"start2\":[170,240,250,300,340,380],\"end2\":[200,210,270,330,370,410],\"identity\":[50,40,100,60,65,20],\"linkID\":[\"0-1\",\"0-2\",\"0-3\",\"0-4\",\"0-5\",\"0-6\"]},\"options\":{\"group\":\"group\",\"curve\":true,\"measure\":\"identity\",\"showLinks\":true,\"label\":true,\"normalColor\":\"#1f77b4\",\"invertedColor\":\"#d62728\",\"useGroupColors\":false,\"colorBar\":true,\"colorBarOptions\":{\"x\":0,\"y\":24,\"width\":10,\"height\":60,\"labelOptions\":{\"fontSize\":8,\"xOffset\":2,\"yOffset\":0},\"titleOptions\":{\"fontSize\":10,\"xOffset\":2,\"yOffset\":0},\"barOptions\":{\"stroke\":\"#000\",\"strokeWidth\":0.5,\"opacity\":1}},\"linkStyle\":{\"stroke\":\"black\",\"strokeWidth\":0.5,\"fillOpacity\":0.4},\"labelStyle\":{\"fontSize\":\"8px\"}}}]},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_normalize.html","id":null,"dir":"Reference","previous_headings":"","what":"Normalize Gene Clusters in a Genomic Chart — GC_normalize","title":"Normalize Gene Clusters in a Genomic Chart — GC_normalize","text":"function normalizes genomic coordinates set genes within cluster, ensuring genes evenly spaced along entire range cluster. function allows option preserve original gene lengths introduce customized gaps genes.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_normalize.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Normalize Gene Clusters in a Genomic Chart — GC_normalize","text":"","code":"GC_normalize(   GC_chart,   group = NULL,   cluster = NULL,   normalize = TRUE,   preserve_gene_length = TRUE,   gap = NULL,   custom_gaps = list() )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_normalize.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Normalize Gene Clusters in a Genomic Chart — GC_normalize","text":"GC_chart chart object containing genomic data clustering information. chart object must include `series` component data cluster. group Column name containing gene names apply custom gaps . cluster vector cluster names normalized. `NULL`, clusters `GC_chart` normalized. normalize logical value indicating whether normalize gene positions within cluster. Default `TRUE`. preserve_gene_length logical vector indicating whether preserve original gene lengths cluster. single value provided, recycled clusters. gap numeric vector specifying proportion total length used gap genes cluster. value must 0 1. single value provided, recycled clusters. `NULL`, gaps calculated based actual spacing genes original data. custom_gaps named list name corresponds gene name value numeric factor adjust gap gene.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_normalize.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Normalize Gene Clusters in a Genomic Chart — GC_normalize","text":"modified `GC_chart` object normalized gene coordinates   specified clusters.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_normalize.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Normalize Gene Clusters in a Genomic Chart — GC_normalize","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 10, 90, 130),   end = c(40, 120, 160, 40, 120, 160),   name = c('Gene 1', 'Gene 2', 'Gene 3','Gene 1', 'Gene 2', 'Gene 3'),   group = c('A', 'B', 'C', 'A', 'B', 'C'),   cluster =  c(1, 1, 1, 2, 2, 2) )  GC_chart(genes_data, group = \"group\", cluster = \"cluster\", height = \"150px\") %>%   GC_normalize(     cluster = 2,     preserve_gene_length = TRUE,     gap = NULL  )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"150px\",\"save_button\":true},\"data\":{\"rowID\":[1,2,3,4,5,6],\"start\":[10,90,130,10,60,110],\"end\":[40,120,160,40,90,140],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"B\",\"C\",\"A\",\"B\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"original_start\":[null,null,null,10,90,130],\"original_end\":[null,null,null,40,120,160]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90,130],\"end\":[40,120,160],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"B\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":75,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":160},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[10,60,110],\"end\":[40,90,140],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"B\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"],\"original_start\":[10,90,130],\"original_end\":[40,120,160]},\"cluster\":[],\"container\":{\"height\":75,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":140},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scale.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Scale of a GC Chart Cluster — GC_scale","title":"Update Scale of a GC Chart Cluster — GC_scale","text":"Modify scale settings specified clusters within GC chart.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scale.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Scale of a GC Chart Cluster — GC_scale","text":"","code":"GC_scale(   GC_chart,   cluster = NULL,   start = NULL,   end = NULL,   padding = 2,   hidden = FALSE,   breaks = list(),   tickValues = NULL,   reverse = FALSE,   axis_position = \"bottom\",   axis_type = \"position\",   y = NULL,   scale_breaks = FALSE,   scale_break_threshold = 20,   scale_break_padding = 1,   ticksCount = 10,   ticksFormat = NULL,   tickStyle = list(),   textStyle = list(),   lineStyle = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scale.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Scale of a GC Chart Cluster — GC_scale","text":"GC_chart GC chart object. cluster Numeric character vector specifying clusters GC chart update. start Numeric vector indicating starting point scale. Default NULL. end Numeric vector indicating end point scale. Default NULL. padding Numeric value percentage string indicating padding either side scale. value can number string format '2%'. Default 2. hidden Logical flag indicating whether axis hidden. Default FALSE. breaks List specifying settings scale breaks. Default empty list (). tickValues Numeric vector NULL, custom tick values used top cluster. NULL, default tick values used. reverse Logical flag indicating whether reverse scale corresponding cluster. Default FALSE. axis_position Character string indicating type axis ('top' bottom'). Default 'bottom'. axis_type Character string indicating type axis ('position' 'range'). Default 'position'. y Numeric value 1 100 indicating y-position x-axis. Default NULL. scale_breaks Logical flag indicating scale breaks employed. Default FALSE. scale_break_threshold Numeric value indicating threshold percentage determining scale breaks. Default 20. scale_break_padding Numeric value indicating padding either side scale break. Default 1. ticksCount Numeric value indicating number ticks scale. Default 10. ticksFormat Format tick labels; depends axis_type, defaulting \",.0f\" 'position' \".2s\" 'range' NULL. tickStyle List specifying style ticks. textStyle List specifying style tick text. lineStyle List specifying style axis line. ... Additional arguments scale settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scale.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Scale of a GC Chart Cluster — GC_scale","text":"Updated GC chart new scale settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scale.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update Scale of a GC Chart Cluster — GC_scale","text":"","code":"genes_data <- data.frame(   start = c(100, 1000, 2000),   end = c(150, 1500, 2500),   name = c('Gene 4', 'Gene 5', 'Gene 6'),   group = c('B', 'A', 'C'),   cluster = c(2, 2, 2) ) #Example usage with all custom options GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"200px\") %>%   GC_scale(     start = 1,     end = 2600,     padding = 2,     hidden = FALSE,     reverse = FALSE,     axis_position = \"bottom\",     # breaks = list(     #  list(start = 160, end = 900),     #  list(start = 1600, end = 1900)     # ),     # tickValues = c(1, 2600),     scale_breaks = TRUE,     scale_break_threshold = 20,     scale_break_padding = 1,     ticksCount = 10,     ticksFormat = \",.0f\",     y = NULL,     tickStyle =       list(         stroke = \"grey\",         strokeWidth = 1,         lineLength = 6         # Any other CSS styles       ),     textStyle =       list(         fill = \"black\",         fontSize = \"10px\",         fontFamily = \"Arial\",         cursor = \"default\"         # Any other CSS styles       ),     lineStyle = list(       stroke = \"grey\",       strokeWidth = 1       # Any other CSS styles     )   ) %>%   GC_legend(FALSE)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[100,1000,2000],\"end\":[150,1500,2500],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"backgroundColor\":\"#0000\"},\"saveButton\":true,\"series\":{\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[100,1000,2000],\"end\":[150,1500,2500],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"start\":1,\"end\":2600,\"xMin\":null,\"xMax\":null,\"padding\":2,\"hidden\":false,\"breaks\":[{\"start\":175.01,\"end\":974.99},{\"start\":1525.01,\"end\":1974.99}],\"tickValues\":null,\"reverse\":false,\"axisPosition\":\"bottom\",\"axisType\":\"position\",\"scale_breaks\":true,\"scale_break_threshold\":20,\"scale_break_padding\":1,\"ticksCount\":10,\"ticksFormat\":\",.0f\",\"y\":null,\"tickStyle\":{\"stroke\":\"grey\",\"strokeWidth\":1,\"lineLength\":6},\"textStyle\":{\"fill\":\"black\",\"fontSize\":\"10px\",\"fontFamily\":\"Arial\",\"cursor\":\"default\"},\"lineStyle\":{\"stroke\":\"grey\",\"strokeWidth\":1}},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scaleBar.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Scale Bar of a GC Chart Cluster — GC_scaleBar","title":"Update Scale Bar of a GC Chart Cluster — GC_scaleBar","text":"Modify scale bar settings specified clusters within GC chart.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scaleBar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Scale Bar of a GC Chart Cluster — GC_scaleBar","text":"","code":"GC_scaleBar(   GC_chart,   show = TRUE,   cluster = NULL,   scaleBarLineStyle = list(),   scaleBarTickStyle = list(),   labelStyle = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scaleBar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Scale Bar of a GC Chart Cluster — GC_scaleBar","text":"GC_chart GC chart object. show Logical. Whether show scale bar. cluster Numeric character vector. Clusters GC chart update. scaleBarLineStyle List style options scale bar line. scaleBarTickStyle List style options scale bar ticks. labelStyle List style options scale bar label. ... Additional arguments scale bar settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scaleBar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Scale Bar of a GC Chart Cluster — GC_scaleBar","text":"Updated GC chart new scale bar settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_scaleBar.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update Scale Bar of a GC Chart Cluster — GC_scaleBar","text":"","code":"genes_data <- data.frame(  start = c(1000, 9000, 13000, 17000, 21000),  end = c(4000, 12000, 16000, 20000, 24000),  name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),  group = c('A', 'B', 'B', 'A', 'C'),  cluster = c(1, 1, 2, 2, 2) )  # Set scale bar for individual clusters GC_chart(genes_data, cluster =\"cluster\", group = \"group\") %>% GC_scaleBar(cluster = 1, title = \"1 kb\", scaleBarUnit = 1000) %>% GC_scaleBar(cluster = 2, title = \"2 kb\", scaleBarUnit = 2000)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"400px\",\"save_button\":true},\"data\":{\"start\":[1000,9000,13000,17000,21000],\"end\":[4000,12000,16000,20000,24000],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[1000,9000],\"end\":[4000,12000],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":1000,\"xMax\":12000},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":{\"show\":true,\"scaleBarLineStyle\":[],\"scaleBarTickStyle\":[],\"labelStyle\":[],\"title\":\"1 kb\",\"scaleBarUnit\":1000},\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[13000,17000,21000],\"end\":[16000,20000,24000],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":13000,\"xMax\":24000},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":{\"show\":true,\"scaleBarLineStyle\":[],\"scaleBarTickStyle\":[],\"labelStyle\":[],\"title\":\"2 kb\",\"scaleBarUnit\":2000},\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Style scale bar GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"400px\") %>%   GC_scaleBar(     title = \"1kb\",     scaleBarUnit = 1000,     cluster = NULL,     x = 0,     y = 50,     labelStyle = list(       labelPosition =  \"left\",       fontSize = \"10px\",       fontFamily = \"sans-serif\",       fill = \"red\", # Text color       cursor = \"default\"       # Any other CSS style for the label     ),     textPadding = -2,     scaleBarLineStyle = list(       stroke = \"black\",       strokeWidth = 1       # Any other CSS style for the line     ),     scaleBarTickStyle = list(       stroke = \"black\",       strokeWidth = 1       # Any other CSS style for the tick     )   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"400px\",\"save_button\":true},\"data\":{\"start\":[1000,9000,13000,17000,21000],\"end\":[4000,12000,16000,20000,24000],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[1000,9000],\"end\":[4000,12000],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":1000,\"xMax\":12000},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":{\"show\":true,\"scaleBarLineStyle\":{\"stroke\":\"black\",\"strokeWidth\":1},\"scaleBarTickStyle\":{\"stroke\":\"black\",\"strokeWidth\":1},\"labelStyle\":{\"labelPosition\":\"left\",\"fontSize\":\"10px\",\"fontFamily\":\"sans-serif\",\"fill\":\"red\",\"cursor\":\"default\"},\"title\":\"1kb\",\"scaleBarUnit\":1000,\"x\":0,\"y\":50,\"textPadding\":-2},\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[13000,17000,21000],\"end\":[16000,20000,24000],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":13000,\"xMax\":24000},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":{\"show\":true,\"scaleBarLineStyle\":{\"stroke\":\"black\",\"strokeWidth\":1},\"scaleBarTickStyle\":{\"stroke\":\"black\",\"strokeWidth\":1},\"labelStyle\":{\"labelPosition\":\"left\",\"fontSize\":\"10px\",\"fontFamily\":\"sans-serif\",\"fill\":\"red\",\"cursor\":\"default\"},\"title\":\"1kb\",\"scaleBarUnit\":1000,\"x\":0,\"y\":50,\"textPadding\":-2},\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_sequence.html","id":null,"dir":"Reference","previous_headings":"","what":"Update Sequence Display of a GC Chart Cluster — GC_sequence","title":"Update Sequence Display of a GC Chart Cluster — GC_sequence","text":"Modify sequence display break markers specified clusters within GC chart.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_sequence.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update Sequence Display of a GC Chart Cluster — GC_sequence","text":"","code":"GC_sequence(   GC_chart,   show = TRUE,   cluster = NULL,   y = 50,   sequenceStyle = list(),   markerStyle = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_sequence.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update Sequence Display of a GC Chart Cluster — GC_sequence","text":"GC_chart GC chart object. show Logical, whether display sequence (default TRUE). cluster Numeric character vector specifying clusters update. y Vertical position sequence line (default 50). sequenceStyle list styling options sequence line. markerStyle list styling options sequence break markers. ... Additional customization arguments sequence display.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_sequence.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update Sequence Display of a GC Chart Cluster — GC_sequence","text":"updated GC chart modified sequence display settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_sequence.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Update Sequence Display of a GC Chart Cluster — GC_sequence","text":"function allows customization sequence line break markers GC chart. offers options adjust sequence line (`sequenceStyle`) break markers (`markerStyle`). `y` parameter can used set vertical position sequence.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_sequence.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update Sequence Display of a GC Chart Cluster — GC_sequence","text":"","code":"genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 2, 2, 2) )  # Basic usage GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"200px\") %>% GC_labels(\"name\") %>% GC_sequence(show = TRUE, y = 50, cluster = NULL)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true,\"y\":50,\"sequenceStyle\":[],\"markerStyle\":[]},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true,\"y\":50,\"sequenceStyle\":[],\"markerStyle\":[]},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Customize sequence and marker styles GC_chart(genes_data, cluster=\"cluster\", group = \"group\", height = \"200px\") %>%   GC_scale(hidden = TRUE, scale_breaks = TRUE) %>%   GC_sequence(     start = NULL,     end = NULL,     sequenceStyle = list(       stroke = \"blue\",       strokeWidth = 1       # Any other CSS style     ),     markerStyle = list(       stroke = \"blue\",       strokeWidth = 1,       gap = 3,       tiltAmount = 5       # Any other CSS style     )   ) %>%   GC_legend(FALSE)  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null},\"backgroundColor\":\"#0000\"},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,90],\"end\":[40,120],\"name\":[\"Gene 1\",\"Gene 3\"],\"group\":[\"A\",\"B\"],\"cluster\":[\"1\",\"1\"],\"rowID\":[1,2],\"strand\":[\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true,\"y\":50,\"sequenceStyle\":{\"stroke\":\"blue\",\"strokeWidth\":1},\"markerStyle\":{\"stroke\":\"blue\",\"strokeWidth\":1,\"gap\":3,\"tiltAmount\":5}},\"scale\":{\"start\":null,\"end\":null,\"xMin\":null,\"xMax\":null,\"padding\":2,\"hidden\":true,\"breaks\":[{\"start\":42.11,\"end\":87.89}],\"tickValues\":null,\"reverse\":false,\"axisPosition\":\"bottom\",\"axisType\":\"position\",\"scale_breaks\":true,\"scale_break_threshold\":20,\"scale_break_padding\":1,\"ticksCount\":10,\"ticksFormat\":null,\"y\":null,\"tickStyle\":[],\"textStyle\":[],\"lineStyle\":[]},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true,\"y\":50,\"sequenceStyle\":{\"stroke\":\"blue\",\"strokeWidth\":1},\"markerStyle\":{\"stroke\":\"blue\",\"strokeWidth\":1,\"gap\":3,\"tiltAmount\":5}},\"scale\":{\"start\":null,\"end\":null,\"xMin\":null,\"xMax\":null,\"padding\":2,\"hidden\":true,\"breaks\":[],\"tickValues\":null,\"reverse\":false,\"axisPosition\":\"bottom\",\"axisType\":\"position\",\"scale_breaks\":true,\"scale_break_threshold\":20,\"scale_break_padding\":1,\"ticksCount\":10,\"ticksFormat\":null,\"y\":null,\"tickStyle\":[],\"textStyle\":[],\"lineStyle\":[]},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_title.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Title to a GC_chart — GC_title","title":"Add Title to a GC_chart — GC_title","text":"Modify cluster title subtitle specified clusters within GC chart adjust display settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_title.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Title to a GC_chart — GC_title","text":"","code":"GC_title(   GC_chart,   title = NULL,   subtitle = NULL,   style = list(),   subtitleFont = list(),   titleFont = list(),   show = TRUE,   height = NULL,   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_title.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Title to a GC_chart — GC_title","text":"GC_chart GC chart object. title Character vector. Titles set clusters. subtitle Character vector. Subtitles set clusters. style list CSS styles applied chart container. element list valid CSS property-value pair. example, list(backgroundColor = \"white\", border = \"2px solid black\"). Default empty list. subtitleFont List. Settings subtitle font. titleFont List. Settings title font. show Logical. Whether display title. Default TRUE. height Character. Height title (e.g., \"50px\"). ... Additional customization arguments title subtitle.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_title.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Title to a GC_chart — GC_title","text":"Updated GC chart new title settings.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_title.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Title to a GC_chart — GC_title","text":"","code":"genes_data <- data.frame(   start = c(10, 50, 90, 130, 170, 210),   end = c(40, 80, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 1, 2, 2, 2) )  # Basic usage GC_chart(genes_data, cluster =\"cluster\", group = \"group\", height = \"400px\") %>% GC_labels(\"name\") %>% GC_title(   title = \"Cluster 1 Data\",   subtitle = \"Detailed View\",   show = TRUE )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"400px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"},\"title\":\"Cluster 1 Data\",\"subtitle\":\"Detailed View\",\"height\":50,\"show\":true},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]} # Customizing title style GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"500px\") %>%   GC_labels(\"name\") %>%   GC_title(     title = \"Cluster 1 Data\",     subtitle = \"Detailed View\",     show = TRUE,     height = \"50px\",     cluster = 1,     x = 0,     y = 25, # height / 2     align = \"center\",     spacing = 20,     style = list(       backgroundColor = \"#0000\"       # Any other CSS styles     ),     titleFont = list(       fontSize = \"16px\",       fontStyle = \"normal\",       fontWeight = \"bold\",       textDecoration = \"normal\",       fontFamily = \"sans-serif\",       cursor = \"default\",       fill = \"black\"       # Any other CSS styles     ),     subtitleFont = list(       fontSize = \"14px\",       fontStyle = \"normal\",       fontWeight = \"bold\",       textDecoration = \"normal\",       fontFamily = \"sans-serif\",       cursor = \"default\",       fill = \"black\"       # Any other CSS styles     )   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"500px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\",\"backgroundColor\":\"#0000\"},\"title\":\"Cluster 1 Data\",\"subtitle\":\"Detailed View\",\"subtitleFont\":{\"fontSize\":\"14px\",\"fontStyle\":\"normal\",\"fontWeight\":\"bold\",\"textDecoration\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"fill\":\"black\"},\"titleFont\":{\"fontSize\":\"16px\",\"fontStyle\":\"normal\",\"fontWeight\":\"bold\",\"textDecoration\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"fill\":\"black\"},\"height\":\"50px\",\"show\":true,\"cluster\":1,\"x\":0,\"y\":25,\"align\":\"center\",\"spacing\":20},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":250,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":250,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true,\"label\":\"name\"},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_tooltip.html","id":null,"dir":"Reference","previous_headings":"","what":"Set Tooltip for a Gene Chart — GC_tooltip","title":"Set Tooltip for a Gene Chart — GC_tooltip","text":"function configures tooltip gene chart.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_tooltip.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set Tooltip for a Gene Chart — GC_tooltip","text":"","code":"GC_tooltip(   GC_chart,   formatter = \"Start:<\/b> {start}
End:<\/b> {end}\",   show = TRUE,   cluster = NULL,   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_tooltip.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set Tooltip for a Gene Chart — GC_tooltip","text":"GC_chart gene chart object modified. formatter character string defining HTML content tooltip. can include placeholders like {start} {end} replaced actual data values. default value shows start end data. show Logical, whether display tooltip . cluster Optional; used specify clusters chart tooltips. ... Additional arguments can used customize tooltip.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_tooltip.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set Tooltip for a Gene Chart — GC_tooltip","text":"Returns gene chart object tooltip configured.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_tooltip.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set Tooltip for a Gene Chart — GC_tooltip","text":"","code":"# Set tooltip genes_data <- data.frame(   start = c(10, 90, 130, 170, 210),   end = c(40, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5'),   group = c('A', 'B', 'B', 'A', 'C') )  # Add tooltips to the gene chart GC_chart(genes_data, group = \"group\", height = \"200px\") %>% GC_tooltip(formatter = \" Start:<\/b> {start}
end:<\/b> {end}\")  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"cluster\":{\"clusterName\":\"cluster\",\"data\":{\"start\":[10,90,130,170,210],\"end\":[40,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\"],\"group\":[\"A\",\"B\",\"B\",\"A\",\"C\"],\"rowID\":[1,2,3,4,5],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"cluster\":[\"cluster\",\"cluster\",\"cluster\",\"cluster\",\"cluster\"]},\"cluster\":[],\"container\":{\"height\":200,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"formatter\":\" Start:<\\/b> {start}
end:<\\/b> {end}\",\"show\":true}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_trackMouse.html","id":null,"dir":"Reference","previous_headings":"","what":"Track Mouse Movement in a GC_chart — GC_trackMouse","title":"Track Mouse Movement in a GC_chart — GC_trackMouse","text":"function enables disables mouse tracking specified clusters within GC chart. enabled, x y coordinates mouse displayed can used place annotations.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_trackMouse.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Track Mouse Movement in a GC_chart — GC_trackMouse","text":"","code":"GC_trackMouse(GC_chart, show = TRUE, cluster = NULL)"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_trackMouse.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Track Mouse Movement in a GC_chart — GC_trackMouse","text":"GC_chart GC chart object annotations added. show Logical, specifies whether track mouse . cluster Numeric character vector specifying clusters annotations added.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_trackMouse.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Track Mouse Movement in a GC_chart — GC_trackMouse","text":"Updated GC chart object mouse tracking settings.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/reference/GC_trackMouse.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Track Mouse Movement in a GC_chart — GC_trackMouse","text":"","code":"genes_data <- data.frame(   start = c(10, 50, 90, 130, 170, 210),   end = c(40, 80, 120, 160, 200, 240),   name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),   group = c('A', 'A', 'B', 'B', 'A', 'C'),   cluster = c(1, 1, 1, 2, 2, 2) )  # Enable mouse tracking GC_chart(genes_data, cluster = \"cluster\", group = \"group\", height = \"220px\") %>% GC_trackMouse()  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"cluster\",\"group\":\"group\",\"width\":\"100%\",\"height\":\"220px\",\"save_button\":true},\"data\":{\"start\":[10,50,90,130,170,210],\"end\":[40,80,120,160,200,240],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\",\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"A\",\"A\",\"B\",\"B\",\"A\",\"C\"],\"cluster\":[\"1\",\"1\",\"1\",\"2\",\"2\",\"2\"],\"rowID\":[1,2,3,4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"]},\"group\":\"group\",\"cluster\":\"cluster\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":\"group\",\"show\":true,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"1\":{\"clusterName\":\"1\",\"data\":{\"start\":[10,50,90],\"end\":[40,80,120],\"name\":[\"Gene 1\",\"Gene 2\",\"Gene 3\"],\"group\":[\"A\",\"A\",\"B\"],\"cluster\":[\"1\",\"1\",\"1\"],\"rowID\":[1,2,3],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":110,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":10,\"xMax\":120},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":true},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"2\":{\"clusterName\":\"2\",\"data\":{\"start\":[130,170,210],\"end\":[160,200,240],\"name\":[\"Gene 4\",\"Gene 5\",\"Gene 6\"],\"group\":[\"B\",\"A\",\"C\"],\"cluster\":[\"2\",\"2\",\"2\"],\"rowID\":[4,5,6],\"strand\":[\"forward\",\"forward\",\"forward\"]},\"cluster\":[],\"container\":{\"height\":110,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":\"group\",\"show\":true},\"sequence\":{\"show\":true},\"scale\":{\"xMin\":130,\"xMax\":240},\"transcript\":{\"group\":\"group\",\"show\":false},\"labels\":{\"group\":\"group\",\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":true},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}}},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_transcript.html","id":null,"dir":"Reference","previous_headings":"","what":"Modify Transcript Characteristics within a Chart — GC_transcript","title":"Modify Transcript Characteristics within a Chart — GC_transcript","text":"function updates chart specific characteristics transcripts based given parameters. can show/hide transcripts, apply color scheme, assign custom colors, filter cluster, accept additional options.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_transcript.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Modify Transcript Characteristics within a Chart — GC_transcript","text":"","code":"GC_transcript(   GC_chart,   transcript = NULL,   type = NULL,   strand = NULL,   group = NULL,   selection = NULL,   show = TRUE,   colorScheme = NULL,   customColors = NULL,   styleExons = list(),   styleIntrons = list(),   styleUTRs = list(),   itemStyleExons = list(),   itemStyleIntrons = list(),   itemStyleUTRs = list(),   labelOptions = list(),   ... )"},{"path":"https://nvelden.github.io/geneviewer/reference/GC_transcript.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Modify Transcript Characteristics within a Chart — GC_transcript","text":"GC_chart chart object modified. transcript Optional column name used clustering transcript data. Default NULL. type Column name identifying feature type (\"UTR\", \"exon\"). Default NULL. strand Optional column name indicating strand orientation. Acceptable values include 1, 'forward', 'sense', '+' represent forward strand, -1, 0, 'reverse', 'antisense', \"complement\" '-' represent reverse strand. Default NULL, meaning strand information used. group Optional column name used transcript grouping influence color aesthetics. selection Numeric character, specific transcript filter transcripts . show Logical, whether show transcripts . colorScheme Character NULL, name color scheme use. customColors List NULL, custom colors apply genes. styleExons List, styles apply exons chart. styleIntrons List, styles apply introns chart. styleUTRs List, styles apply UTRs chart. itemStyleExons List, list styles apply individual exons chart. itemStyleIntrons List, list styles apply individual introns chart. itemStyleUTRs List, list styles apply individual UTRs chart. labelOptions List, options styling labels font size, color, position. ... Additional arguments passed gene options.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_transcript.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Modify Transcript Characteristics within a Chart — GC_transcript","text":"Returns modified gene chart object.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/GC_transcript.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Modify Transcript Characteristics within a Chart — GC_transcript","text":"","code":"transcript_data <- data.frame(   transcript = c(\"transcript1\", \"transcript1\", \"transcript1\", \"transcript1\",                  \"transcript2\", \"transcript2\", \"transcript2\"),   type = c(\"5_utr\", \"exon\", \"exon\", \"3_utr\",            \"5_utr\", \"exon\", \"3_utr\"),   start = c(1, 101, 201, 301,             1, 101, 301),   end = c(50, 150, 250, 350,           50, 150, 350),   strand = rep(\"forward\", 7) )  # All default transcript settings GC_chart(   transcript_data,   start = \"start\",   end = \"end\",   height = \"200px\" ) %>%   GC_transcript(     transcript = \"transcript\",     strand = \"strand\",     type = \"type\",     group = NULL,     show = TRUE,     selection = NULL,     colorScheme = NULL,     customColors = NULL,     styleExons = list(       show = TRUE,       strokeWidth = 0,       cursor = \"default\",       marker = \"box\",       markerSize = \"medium\",       arrowheadWidth = NULL,       arrowheadHeight = NULL,       markerHeight = NULL,       cornerRadius = NULL       # Any other CSS style     ),     styleIntrons = list(       show = TRUE,       strokeWidth = 1,       fill = \"none\",       cursor = \"default\",       marker = \"intron\",       markerSize = \"medium\",       arrowheadWidth = NULL,       arrowheadHeight = NULL,       markerHeight = NULL,       cornerRadius = NULL       # Any other CSS style     ),     styleUTRs = list(       show = TRUE,       fontSize = \"10px\",       fontStyle = \"normal\",       fontFamily = \"sans-serif\",       cursor = \"default\",       color = \"black\",       fill = \"#FFF\",       strokeWidth = 1,       marker = \"box\",       markerSize = \"medium\",       arrowheadWidth = NULL,       arrowheadHeight = NULL,       markerHeight = NULL,       cornerRadius = NULL       # Any other CSS style     ),     labelOptions = list(       show = TRUE,       xOffset = 2,       yOffset = 0,       fontSize = \"12px\",       fontStyle = \"normal\",       fontWeight = \"normal\",       fontFamily = \"sans-serif\",       cursor = \"default\",       color = \"black\"     ),     itemStyleExons = list(),     itemStyleIntrons = list(),     itemStyleUTRs = list()   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"transcript\",\"strand\":\"strand\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"transcript\":[\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\"],\"type\":[\"5_utr\",\"intron\",\"exon\",\"intron\",\"exon\",\"intron\",\"3_utr\",\"5_utr\",\"intron\",\"exon\",\"intron\",\"3_utr\"],\"start\":[1,51,101,151,201,251,301,1,51,101,151,301],\"end\":[50,100,150,200,250,300,350,50,100,150,300,350],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"rowID\":[1,2,3,4,5,6,7,8,9,10,11,12]},\"cluster\":\"transcript\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":null,\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"transcript1\":{\"clusterName\":\"transcript1\",\"data\":{\"transcript\":[\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\"],\"type\":[\"5_utr\",\"intron\",\"exon\",\"intron\",\"exon\",\"intron\",\"3_utr\"],\"start\":[1,51,101,151,201,251,301],\"end\":[50,100,150,200,250,300,350],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"rowID\":[1,2,3,4,5,6,7],\"cluster\":[\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":false},\"sequence\":{\"show\":false},\"scale\":{\"xMin\":1,\"xMax\":350},\"transcript\":{\"show\":true,\"styleExons\":{\"show\":true,\"strokeWidth\":0,\"cursor\":\"default\",\"marker\":\"box\",\"markerSize\":\"medium\",\"arrowheadWidth\":null,\"arrowheadHeight\":null,\"markerHeight\":null,\"cornerRadius\":null},\"styleIntrons\":{\"show\":true,\"strokeWidth\":1,\"fill\":\"none\",\"cursor\":\"default\",\"marker\":\"intron\",\"markerSize\":\"medium\",\"arrowheadWidth\":null,\"arrowheadHeight\":null,\"markerHeight\":null,\"cornerRadius\":null},\"styleUTRs\":{\"show\":true,\"fontSize\":\"10px\",\"fontStyle\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"color\":\"black\",\"fill\":\"#FFF\",\"strokeWidth\":1,\"marker\":\"box\",\"markerSize\":\"medium\",\"arrowheadWidth\":null,\"arrowheadHeight\":null,\"markerHeight\":null,\"cornerRadius\":null},\"labelOptions\":{\"show\":true,\"xOffset\":2,\"yOffset\":0,\"fontSize\":\"12px\",\"fontStyle\":\"normal\",\"fontWeight\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"color\":\"black\"}},\"labels\":{\"group\":null,\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"transcript2\":{\"clusterName\":\"transcript2\",\"data\":{\"transcript\":[\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\"],\"type\":[\"5_utr\",\"intron\",\"exon\",\"intron\",\"3_utr\"],\"start\":[1,51,101,151,301],\"end\":[50,100,150,300,350],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"rowID\":[8,9,10,11,12],\"cluster\":[\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":false},\"sequence\":{\"show\":false},\"scale\":{\"xMin\":1,\"xMax\":350},\"transcript\":{\"show\":true,\"styleExons\":{\"show\":true,\"strokeWidth\":0,\"cursor\":\"default\",\"marker\":\"box\",\"markerSize\":\"medium\",\"arrowheadWidth\":null,\"arrowheadHeight\":null,\"markerHeight\":null,\"cornerRadius\":null},\"styleIntrons\":{\"show\":true,\"strokeWidth\":1,\"fill\":\"none\",\"cursor\":\"default\",\"marker\":\"intron\",\"markerSize\":\"medium\",\"arrowheadWidth\":null,\"arrowheadHeight\":null,\"markerHeight\":null,\"cornerRadius\":null},\"styleUTRs\":{\"show\":true,\"fontSize\":\"10px\",\"fontStyle\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"color\":\"black\",\"fill\":\"#FFF\",\"strokeWidth\":1,\"marker\":\"box\",\"markerSize\":\"medium\",\"arrowheadWidth\":null,\"arrowheadHeight\":null,\"markerHeight\":null,\"cornerRadius\":null},\"labelOptions\":{\"show\":true,\"xOffset\":2,\"yOffset\":0,\"fontSize\":\"12px\",\"fontStyle\":\"normal\",\"fontWeight\":\"normal\",\"fontFamily\":\"sans-serif\",\"cursor\":\"default\",\"color\":\"black\"}},\"labels\":{\"group\":null,\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}},\"transcript_called\":true},\"evals\":[],\"jsHooks\":[]}# Change the appearance of a specific intron GC_chart(transcript_data,          start = \"start\",          end = \"end\",          height = \"200px\" ) %>%   GC_transcript(     transcript = \"transcript\",     type = \"type\",     selection = 2,     itemStyleExons = list(list(index = 0, fill = \"red\")     )   )  {\"x\":{\"params\":{\"start\":\"start\",\"end\":\"end\",\"cluster\":\"transcript\",\"width\":\"100%\",\"height\":\"200px\",\"save_button\":true},\"data\":{\"transcript\":[\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\"],\"type\":[\"5_utr\",\"intron\",\"exon\",\"intron\",\"exon\",\"intron\",\"3_utr\",\"5_utr\",\"intron\",\"exon\",\"intron\",\"3_utr\"],\"start\":[1,51,101,151,201,251,301,1,51,101,151,301],\"end\":[50,100,150,200,250,300,350,50,100,150,300,350],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"rowID\":[1,2,3,4,5,6,7,8,9,10,11,12]},\"cluster\":\"transcript\",\"graphContainer\":{\"direction\":\"column\"},\"style\":[],\"title\":{\"style\":{\"width\":\"100%\"}},\"legend\":{\"group\":null,\"show\":false,\"position\":\"bottom\",\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"saveButton\":true,\"series\":{\"transcript1\":{\"clusterName\":\"transcript1\",\"data\":{\"transcript\":[\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\"],\"type\":[\"5_utr\",\"intron\",\"exon\",\"intron\",\"exon\",\"intron\",\"3_utr\"],\"start\":[1,51,101,151,201,251,301],\"end\":[50,100,150,200,250,300,350],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"rowID\":[1,2,3,4,5,6,7],\"cluster\":[\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\",\"transcript1\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":false},\"sequence\":{\"show\":false},\"scale\":{\"xMin\":1,\"xMax\":350},\"transcript\":{\"group\":null,\"show\":true},\"labels\":{\"group\":null,\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}},\"transcript2\":{\"clusterName\":\"transcript2\",\"data\":{\"transcript\":[\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\"],\"type\":[\"5_utr\",\"intron\",\"exon\",\"intron\",\"3_utr\"],\"start\":[1,51,101,151,301],\"end\":[50,100,150,300,350],\"strand\":[\"forward\",\"forward\",\"forward\",\"forward\",\"forward\"],\"rowID\":[8,9,10,11,12],\"cluster\":[\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\",\"transcript2\"]},\"cluster\":[],\"container\":{\"height\":100,\"width\":\"100%\",\"style\":{\"width\":\"100%\",\"backgroundColor\":null}},\"genes\":{\"group\":null,\"show\":false},\"sequence\":{\"show\":false},\"scale\":{\"xMin\":1,\"xMax\":350},\"transcript\":{\"show\":true,\"itemStyleExons\":[{\"index\":0,\"fill\":\"red\"}]},\"labels\":{\"group\":null,\"show\":true},\"coordinates\":{\"show\":false},\"scaleBar\":[],\"footer\":[],\"clusterLabel\":[],\"clusterTitle\":[],\"annotations\":[],\"trackMouse\":{\"show\":false},\"tooltip\":{\"show\":true,\"formatter\":\"Start:<\\/b> {start}
End:<\\/b> {end}\"}}},\"transcript_called\":true},\"evals\":[],\"jsHooks\":[]}"},{"path":"https://nvelden.github.io/geneviewer/reference/erythromycin_BlastP.html","id":null,"dir":"Reference","previous_headings":"","what":"Erythromycin BlastP results — erythromycin_BlastP","title":"Erythromycin BlastP results — erythromycin_BlastP","text":"dataset contains detailed information genes involved biosynthesis Erythromycin, antibiotic produced bacterium Saccharopolyspora erythraea several homologous gene clusters identified antiSMASH. includes gene identifiers, chromosomal positions, orientations, annotations regarding products functions, well similarity identity scores BlastP analysis.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/erythromycin_BlastP.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Erythromycin BlastP results — erythromycin_BlastP","text":"","code":"erythromycin_BlastP"},{"path":"https://nvelden.github.io/geneviewer/reference/erythromycin_BlastP.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Erythromycin BlastP results — erythromycin_BlastP","text":"data frame 148 observations 16 variables: protein_id Unique protein identifiers. character vector. region chromosomal region gene, indicating start end positions strand. character vector. translation Amino acid sequence protein encoded gene. character vector. cluster Identifier gene cluster gene belongs. character vector. strand strand orientation (\"forward\" \"complement\") gene. character vector. start start position gene chromosome. numeric vector. end end position gene chromosome. numeric vector. rowID unique identifier row dataset. integer vector. identity identity score BlastP analysis, representing percentage identical matches. numeric vector. similarity similarity score BlastP analysis, often reflecting functional structural similarity. numeric vector. BlastP Reference protein_id BlastP comparison, NA applicable. character vector. score Score assigned based BlastP analysis, quantifying match quality. numeric vector. Gene Gene name identifier available, otherwise NA. character vector. Position Formatted string indicating gene's position orientation chromosome. character vector. Product Description gene product. character vector. Functions Functional categorization gene. character vector.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/erythromycin_BlastP.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Erythromycin BlastP results — erythromycin_BlastP","text":"Derived BlastP analysis Saccharopolyspora erythraea genes   involved Erythromycin production.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/erythromycin_cluster.html","id":null,"dir":"Reference","previous_headings":"","what":"Erythromycin Gene Cluster Data — erythromycin_cluster","title":"Erythromycin Gene Cluster Data — erythromycin_cluster","text":"dataset contains information various genes involved biosynthesis Erythromycin, antibiotic produced bacterium Saccharopolyspora erythraea. includes details gene identifiers, start end positions genes, associated functions products.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/erythromycin_cluster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Erythromycin Gene Cluster Data — erythromycin_cluster","text":"","code":"erythromycin_cluster"},{"path":"https://nvelden.github.io/geneviewer/reference/erythromycin_cluster.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Erythromycin Gene Cluster Data — erythromycin_cluster","text":"data frame 23 rows 6 columns: Identifiers Unique identifiers genes. character vector. Start Start positions genes chromosome. numeric vector. End End positions genes chromosome. numeric vector. Strand Strand orientation gene, either \"+\" \"-\". character vector. Product Description gene products. character vector. Functions Functional categorization genes. character vector.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/gbk_features_to_df.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert GenBank Features to Data Frame — gbk_features_to_df","title":"Convert GenBank Features to Data Frame — gbk_features_to_df","text":"function processes list GenBank features (loaded read_gbk()) converts selected features data frame. supports processing multiple gene clusters.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/gbk_features_to_df.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert GenBank Features to Data Frame — gbk_features_to_df","text":"","code":"gbk_features_to_df(   gbk_list,   feature = \"CDS\",   keys = NULL,   process_region = TRUE )"},{"path":"https://nvelden.github.io/geneviewer/reference/gbk_features_to_df.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert GenBank Features to Data Frame — gbk_features_to_df","text":"gbk_list list lists sub-list contains GenBank features specific gene cluster. sub-list expected named list features, feature character vector. feature string specifying feature type extract gene cluster's FEATURE list (e.g., \"CDS\" \"gene\"). Defaults \"CDS\". keys optional vector strings representing specific keys within feature retain final data frame. `NULL` (default), keys within specified feature included. process_region boolean flag; set `TRUE` (default), special processing performed 'region' key (present) extract 'strand', 'start', 'end' information.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/gbk_features_to_df.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert GenBank Features to Data Frame — gbk_features_to_df","text":"data frame row corresponds feature input   list. data frame includes 'cluster' column indicating source gbk   file.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/gbk_features_to_df.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert GenBank Features to Data Frame — gbk_features_to_df","text":"","code":"if (FALSE) { gbk <- read_gbk(\"path/to/genbank_file.gbk\") df <- gbk_features_to_df(gbk)  # To extract only specific keys within the \"CDS\" feature df <- gbk_features_to_df(gbk, feature = \"CDS\", keys = c(\"gene\", \"region\"))  # To disable special processing of the 'region' key df <- gbk_features_to_df(gbk, process_region = FALSE) }"},{"path":"https://nvelden.github.io/geneviewer/reference/genbank_to_fasta.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert GenBank to FASTA Format — genbank_to_fasta","title":"Convert GenBank to FASTA Format — genbank_to_fasta","text":"function reads GenBank file, extracts sequence writes new file FASTA format. parses DEFINITION VERSION header sequences ORIGIN section.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/genbank_to_fasta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert GenBank to FASTA Format — genbank_to_fasta","text":"","code":"genbank_to_fasta(path, output_dir = NULL)"},{"path":"https://nvelden.github.io/geneviewer/reference/genbank_to_fasta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert GenBank to FASTA Format — genbank_to_fasta","text":"path Path GenBank file. output_dir Optional path output FASTA file. NULL, output saved directory input file base name .fasta extension.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/genbank_to_fasta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert GenBank to FASTA Format — genbank_to_fasta","text":"None explicitly, writes FASTA formatted data file.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/genbank_to_fasta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert GenBank to FASTA Format — genbank_to_fasta","text":"","code":"if (FALSE) { genbank_to_fasta(\"path/to/input.gb\") }"},{"path":"https://nvelden.github.io/geneviewer/reference/geneviewer-shiny.html","id":null,"dir":"Reference","previous_headings":"","what":"Shiny bindings for geneviewer — geneviewer-shiny","title":"Shiny bindings for geneviewer — geneviewer-shiny","text":"Output render functions using geneviewer within Shiny applications interactive Rmd documents.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/geneviewer-shiny.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shiny bindings for geneviewer — geneviewer-shiny","text":"","code":"GC_chartOutput(outputId, width = \"100%\", height = \"400px\")  renderGC_chart(expr, env = parent.frame(), quoted = FALSE)"},{"path":"https://nvelden.github.io/geneviewer/reference/geneviewer-shiny.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shiny bindings for geneviewer — geneviewer-shiny","text":"outputId Output variable read . width, height Must valid CSS unit (like '100 number, coerced string 'px' appended. height Height output widget, must valid CSS unit (like '100 'px' appended. expr expression generates GC chart. env environment evaluate expr. quoted expr quoted expression (quote())? useful want save expression variable.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/geneviewer-shiny.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shiny bindings for geneviewer — geneviewer-shiny","text":"GC_chart widget can placed UI.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/reference/geneviewer-shiny.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Shiny bindings for geneviewer — geneviewer-shiny","text":"","code":"if (interactive()) {   library(shiny)   library(geneviewer)    ui <- fluidPage(     titlePanel(\"Omphalotin Gene Cluster Visualization\"),     mainPanel(       GC_chartOutput(\"gcChart\", width = \"100%\", height = \"500px\")     )   )    server <- function(input, output) {     output$gcChart <- renderGC_chart({       GC_chart(         ophA_clusters, # Ensure 'ophA_clusters' data is defined or available         cluster = \"cluster\",         group = \"class\"       ) %>%       GC_title(title = c(\"O. olearius<\/i>\", \"D. bispora<\/i>\")) %>%       GC_labels(\"name\") %>%       GC_legend(position = \"bottom\") %>%       GC_scaleBar() %>%       GC_clusterLabel(title = \"ophA\")     })   }    shinyApp(ui = ui, server = server) }"},{"path":"https://nvelden.github.io/geneviewer/reference/get_introns.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Intron Positions Based on Exons — get_introns","title":"Calculate Intron Positions Based on Exons — get_introns","text":"function takes dataset containing transcript information calculates start end positions introns based positions exons. generates combined dataframe including original exons calculated introns.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/get_introns.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Intron Positions Based on Exons — get_introns","text":"","code":"get_introns(data)"},{"path":"https://nvelden.github.io/geneviewer/reference/get_introns.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Intron Positions Based on Exons — get_introns","text":"data dataframe containing `start` `end` positions transcripts. Optional columns `type` (exon UTR), `transcript` (containing unique transcript IDs), `strand` (indicating direction, forward reverse, transcript).","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/get_introns.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Intron Positions Based on Exons — get_introns","text":"dataframe original exons calculated introns, sorted   transcript start position. row includes `start`, `end`,   `type` (exon, UTR intron), `transcript`, `strand` segment.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/hs_dystrophin_transcripts.html","id":null,"dir":"Reference","previous_headings":"","what":"Human Dystrophin Transcripts Data — hs_dystrophin_transcripts","title":"Human Dystrophin Transcripts Data — hs_dystrophin_transcripts","text":"dataset contains Exon positions human Dystrophin transcripts 'Dp427p2', 'Dp260-2', 'Dp140', 'Dp116', 'Dp71'.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/hs_dystrophin_transcripts.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Human Dystrophin Transcripts Data — hs_dystrophin_transcripts","text":"","code":"hs_dystrophin_transcripts"},{"path":"https://nvelden.github.io/geneviewer/reference/hs_dystrophin_transcripts.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Human Dystrophin Transcripts Data — hs_dystrophin_transcripts","text":"data frame 202 rows 5 columns: transcript Transcript names. character vector representing   names transcripts. type Transcript type. start Start positions. integer vector showing starting   positions Exon. end End positions. integer vector showing ending   positions Exon. length Transcript lengths. integer vector   indicating length transcript.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/human_hox_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Human HOX Gene Cluster Data — human_hox_genes","title":"Human HOX Gene Cluster Data — human_hox_genes","text":"dataset represents positions clusters various human HOX genes. HOX genes group related genes control body plan embryo along head-tail axis. dataset includes genes HOXA, HOXB, HOXC, HOXD clusters.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/human_hox_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Human HOX Gene Cluster Data — human_hox_genes","text":"","code":"human_hox_genes"},{"path":"https://nvelden.github.io/geneviewer/reference/human_hox_genes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Human HOX Gene Cluster Data — human_hox_genes","text":"data frame 39 rows 6 columns: symbol HGNC symbols HOX genes. character vector. chromosome_name Chromosome number gene located. numeric vector. start Start positions genes chromosome. numeric vector. end End positions genes chromosome. numeric vector. strand -1 reverse 1 forward. cluster Cluster identification character vector,   specifying HOX gene cluster (HOXA, HOXB, HOXC, HOXD). name Simplified names HOX genes. character vector.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/mummer_alignment.html","id":null,"dir":"Reference","previous_headings":"","what":"Perform Sequence Alignment Using MUMmer — mummer_alignment","title":"Perform Sequence Alignment Using MUMmer — mummer_alignment","text":"function orchestrates alignment sequences specified directory using MUMmer, tool aligning large DNA protein sequences. can handle GenBank FASTA file formats. performs checks ensure necessary files present.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/mummer_alignment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Perform Sequence Alignment Using MUMmer — mummer_alignment","text":"","code":"mummer_alignment(   path,   cluster = NULL,   maptype = \"many-to-many\",   seqtype = \"protein\",   mummer_options = \"\",   filter_options = \"\",   remove_files = TRUE,   output_dir = NULL )"},{"path":"https://nvelden.github.io/geneviewer/reference/mummer_alignment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Perform Sequence Alignment Using MUMmer — mummer_alignment","text":"path directory containing sequence files. cluster Optional vector cluster names consider alignment. NULL, clusters inferred file names. order names determines alignment sequence. maptype type mapping perform; \"many--many\" \"one--one\". \"many--many\" allows multiple matches clusters, \"one--one\" restricts alignments unique matches pair. seqtype type sequences, either \"protein\" \"nucleotide\". mummer_options Additional command line options MUMmer. see available options, can run `nucmer --help` `promer --help` terminal depending whether aligning nucleotide protein sequences. filter_options Additional options filtering MUMmer results. view filtering options, run `delta-filter --help` terminal. remove_files Logical indicating whether remove intermediate files generated process, defaults TRUE. output_dir Optional directory save output files; defaults NULL, uses input file directory outputs.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/mummer_alignment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Perform Sequence Alignment Using MUMmer — mummer_alignment","text":"data frame combining alignment results, NULL errors occur   processing.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/mummer_alignment.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Perform Sequence Alignment Using MUMmer — mummer_alignment","text":"Kurtz S, Phillippy , Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL (2004). Versatile open software comparing large genomes. Genome Biology, 5(R12).","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/mummer_alignment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Perform Sequence Alignment Using MUMmer — mummer_alignment","text":"","code":"if (FALSE) { # Basic alignment with default options mummer_alignment(   path = \"/path/to/sequences\",   maptype = \"many-to-many\",   seqtype = \"protein\" ) # Alignment with specific MUMmer options mummer_alignment(   path = \"/path/to/sequences\", maptype = \"one-to-one\", seqtype = \"protein\",   mummer_options = \"--maxgap=500 --mincluster=100\",   filter_options = \"-i 90\"   )  }"},{"path":"https://nvelden.github.io/geneviewer/reference/ophA_clusters.html","id":null,"dir":"Reference","previous_headings":"","what":"ophA Gene Cluster from Omphalotus olearius — ophA_clusters","title":"ophA Gene Cluster from Omphalotus olearius — ophA_clusters","text":"dataset represents ophA gene cluster Omphalotus olearius Dendrothele bispora, involved production omphalotin, cyclic N-methylated peptide.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/ophA_clusters.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"ophA Gene Cluster from Omphalotus olearius — ophA_clusters","text":"","code":"ophA_clusters"},{"path":"https://nvelden.github.io/geneviewer/reference/ophA_clusters.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"ophA Gene Cluster from Omphalotus olearius — ophA_clusters","text":"data frame 17 rows 5 columns: name Gene names. character vector. start Start positions genes. integer vector. end End positions genes. integer vector. class Classifications genes. character vector indicating   type protein function associated gene. cluster Cluster identification character vector, specifying whether   gene belongs ophA dbophA gene cluster.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/ophA_clusters.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"ophA Gene Cluster from Omphalotus olearius — ophA_clusters","text":"van der Velden NS et al. Autocatalytic backbone N-methylation family ribosomal peptide natural products. Nat Chem Biol. 2017 Aug;13(8):833-835. doi: 10.1038/nchembio.2393. Epub 2017 Jun 5. PMID: 28581484.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/protein_blast.html","id":null,"dir":"Reference","previous_headings":"","what":"Perform Protein BLAST Analysis Within Specified Clusters — protein_blast","title":"Perform Protein BLAST Analysis Within Specified Clusters — protein_blast","text":"function conducts BLAST analysis protein sequences within specified clusters. generates possible protein combinations query cluster clusters, performs pairwise alignments, calculates sequence identity similarity, filters results based minimum identity threshold.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/protein_blast.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Perform Protein BLAST Analysis Within Specified Clusters — protein_blast","text":"","code":"protein_blast(   data,   query,   id = \"protein_id\",   start = \"start\",   end = \"end\",   cluster = \"cluster\",   genes = NULL,   identity = 30,   parallel = TRUE )"},{"path":"https://nvelden.github.io/geneviewer/reference/protein_blast.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Perform Protein BLAST Analysis Within Specified Clusters — protein_blast","text":"data dataframe character vector specifying path .gbk files. character vector provided, interpreted file paths .gbk files read processed. dataframe must contain columns unique protein identifiers, cluster identifiers, protein sequences, start end positions gene. query name query cluster used BLAST comparisons. id name column contains gene identifiers. Defaults \"protein_id\". start name column specifying start positions genes. Defaults \"start\". end name column specifying end positions genes. Defaults \"end\". cluster name column specifying cluster names. Defaults \"cluster\". genes optional vector gene identifiers include analysis. Defaults NULL. identity Minimum identity threshold BLAST hits considered significant. Defaults 30. parallel Logical indicating whether use parallel processing alignments. Defaults TRUE.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/protein_blast.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Perform Protein BLAST Analysis Within Specified Clusters — protein_blast","text":"modified version input `data` dataframe, including   additional columns BLAST results (identity, similarity).","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/protein_blast.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Perform Protein BLAST Analysis Within Specified Clusters — protein_blast","text":"function relies Biostrings pwalign package sequence alignment dplyr package data manipulation. Ensure packages installed loaded R session.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/protein_blast.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Perform Protein BLAST Analysis Within Specified Clusters — protein_blast","text":"","code":"if (FALSE) { path_to_folder <- \"path/to/gbk/folder/\" data_updated <- protein_blast(                          path_to_folder,                          id = \"protein_id\",                          query = \"cluster A\",                          identity = 30                          ) }"},{"path":"https://nvelden.github.io/geneviewer/reference/read_bed.html","id":null,"dir":"Reference","previous_headings":"","what":"Read BED Files — read_bed","title":"Read BED Files — read_bed","text":"function reads BED files specified directory file path combines single data frame. BED files use 0-based coordinate starts, function transforms coordinates 1-based import.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_bed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read BED Files — read_bed","text":"","code":"read_bed(path)"},{"path":"https://nvelden.github.io/geneviewer/reference/read_bed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read BED Files — read_bed","text":"path character string specifying directory containing BED files file path single BED file.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_bed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read BED Files — read_bed","text":"data frame combining data BED files.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_bed.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read BED Files — read_bed","text":"function can read multiple BED files directory   single BED file specified path. adds 'filename' column   name file, combines data frames files one.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_bed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read BED Files — read_bed","text":"","code":"if (FALSE) { # Read BED files from a directory bed_data <- read_bed(\"path/to/directory\")  # Read a single BED file bed_data <- read_bed(\"path/to/file.bed\") }"},{"path":"https://nvelden.github.io/geneviewer/reference/read_fasta.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Protein Sequences from FASTA Files — read_fasta","title":"Read Protein Sequences from FASTA Files — read_fasta","text":"function reads protein sequences specified FASTA file FASTA files within directory. specifically looks metadata FASTA headers key-value pairs separated equals sign `=`. example, header '>protein1 [gene=scnD] [protein=ScnD]', extracts 'gene' key 'scnD' value, similarly key-value pairs.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_fasta.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Protein Sequences from FASTA Files — read_fasta","text":"","code":"read_fasta(fasta_path, sequence = TRUE, keys = NULL, file_extension = \"fasta\")"},{"path":"https://nvelden.github.io/geneviewer/reference/read_fasta.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Protein Sequences from FASTA Files — read_fasta","text":"fasta_path Path FASTA file directory containing FASTA files. sequence Logical; `TRUE`, protein sequences included returned data frame. keys optional vector strings representing specific keys within fasta header retain final data frame. `NULL` (default), keys within specified feature included. file_extension Extension FASTA files read directory (default 'fasta').","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_fasta.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Protein Sequences from FASTA Files — read_fasta","text":"data frame columns piece information extracted  FASTA headers.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_fasta.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read Protein Sequences from FASTA Files — read_fasta","text":"Biostrings package required run function.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_fasta.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Protein Sequences from FASTA Files — read_fasta","text":"","code":"if (FALSE) { # Read sequences from a single FASTA file sequences_df <- read_fasta(\"path/to/single_file.fasta\")  # Read all sequences from a directory of FASTA files sequences_df <- read_fasta(\"path/to/directory/\", file_extension = \"fa\")  # Read sequences and include the protein sequences in the output sequences_df <- read_fasta(\"path/to/directory/\", sequence = TRUE) }"},{"path":"https://nvelden.github.io/geneviewer/reference/read_gbk.html","id":null,"dir":"Reference","previous_headings":"","what":"Read Data from GenBank Files — read_gbk","title":"Read Data from GenBank Files — read_gbk","text":"function reads data single GenBank file directorty GenBank files. allows selective extraction information specifying sections features.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_gbk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read Data from GenBank Files — read_gbk","text":"","code":"read_gbk(path, sections = NULL, features = NULL, origin = TRUE)"},{"path":"https://nvelden.github.io/geneviewer/reference/read_gbk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read Data from GenBank Files — read_gbk","text":"path string representing file path target GenBank (.gbk) file directory. sections optional vector strings representing names specific sections within GenBank file extract (e.g., \"LOCUS\", \"DEFINITION\", \"ACCESSION\", \"VERSION\"). `NULL` (default), function extracts available sections. features optional vector strings indicating specific feature types extract FEATURES section GenBank file (e.g., \"CDS\", \"gene\", \"mRNA\"). `NULL` (default), function extracts feature types present FEATURES section. origin boolean flag; set `TRUE` (default), origin sequence data included output.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_gbk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read Data from GenBank Files — read_gbk","text":"list containing contents specified sections features   GenBank file. section feature returned separate   list element.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_gbk.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read Data from GenBank Files — read_gbk","text":"","code":"if (FALSE) { # Read all data from a GenBank file gbk_data <- read_gbk(\"path/to/genbank_file.gbk\")  # Read all data from a directory of GenBank files gbk_data <- read_gbk(\"path/to/genbank/directory\")  # Read only specific sections from a GenBank file gbk_data <- read_gbk(   \"path/to/genbank_file.gbk\",   sections = c(\"LOCUS\", \"DEFINITION\") )  # Read specific features from the FEATURES section of a GenBank file gbk_data <- read_gbk(\"path/to/genbank_file.gbk\", features = c(\"gene\", \"CDS\"))  # Read data without the origin sequence gbk_data <- read_gbk(\"path/to/genbank_file.gbk\", origin = FALSE) }"},{"path":"https://nvelden.github.io/geneviewer/reference/read_gff.html","id":null,"dir":"Reference","previous_headings":"","what":"Read GFF Files — read_gff","title":"Read GFF Files — read_gff","text":"function reads GFF files specified directory file path combines single data frame.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_gff.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read GFF Files — read_gff","text":"","code":"read_gff(path, fields = NULL)"},{"path":"https://nvelden.github.io/geneviewer/reference/read_gff.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read GFF Files — read_gff","text":"path character string specifying directory containing GFF files file path single GFF file. fields optional vector character strings specifying fields extract GFF files.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_gff.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read GFF Files — read_gff","text":"data frame containing combined data GFF files.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_gff.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read GFF Files — read_gff","text":"function can read multiple GFF files directory   single GFF file. processes file, extracts specified fields (  provided), adds 'name' column filename, combines data   frames files one.","code":""},{"path":"https://nvelden.github.io/geneviewer/reference/read_gff.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read GFF Files — read_gff","text":"","code":"if (FALSE) { # Read GFF files from a directory gff_data <- read_gff(\"path/to/directory\")  # Read a single GFF file gff_data <- read_gff(\"path/to/file.gff\")  # Read specific fields from GFF files gff_data <- read_gff( \"path/to/directory\", fields = c(\"seqid\", \"start\", \"end\", \"attributes\") ) }"},{"path":"https://nvelden.github.io/geneviewer/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. magrittr %>%","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-8","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.8","text":"Option display transcripts using GC_transcripts function.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-7","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.7","text":"Option perform MUMmer alignments. Add option add color bar.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-6","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.6","text":"Option perfrom BlastP gene clusters. Add option add links genes clusters.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-5","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.5","text":"Add preset markers genes: arrow, boxarrow, box, cbox rbox. Add options load cluster information GenBank FASTA files.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-4","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.4","text":"Add option add gene links. Change package name GCVieweR geneviewer.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-3","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.3","text":"Option align specified gene across clusters.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-2","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.2","text":"Options add text, line, arrow, rectangle, symbol, terminator promoter annotations GC_chart.","code":""},{"path":[]},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"enhancements-0-1-1","dir":"Changelog","previous_headings":"","what":"Enhancements:","title":"geneviewer 0.1.1","text":"Introduced customizable margin settings charts, clusters, titles, legends. Added styling options containers charts, clusters, titles, legends. Implemented new feature display clusters side side. Updated expanded documentation reflect new features usability improvements.","code":""},{"path":"https://nvelden.github.io/geneviewer/news/index.html","id":"geneviewer-010","dir":"Changelog","previous_headings":"","what":"geneviewer 0.1.0","title":"geneviewer 0.1.0","text":"Initial Beta release.","code":""}]