Update documentation and examples

DESCRIPTION

@@ -4,11 +4,12 @@ Title: Gene Cluster Visualizations in R
 Version: 0.1.7
 Author: Niels van der Velden
 Maintainer: Niels van der Velden <[email protected]>
-Description: 'geneviewer' is an R package for plotting gene clusters. 
-              It imports data from GenBank, FASTA, and GFF files, performs BlastP
-              and MUMmer alignments, and displays results on gene arrow maps. 
-              The package offers extensive customization options, including 
-              legends, labels, annotations, scales, colors, tooltips, and more.
+Description: 'geneviewer' is an R package for plotting gene clusters and 
+              transcripts.It imports data from GenBank, FASTA, and GFF files, 
+              performs BlastP and MUMmer alignments, and displays results on 
+              gene arrow maps. The package offers extensive customization 
+              options, including legends, labels, annotations, scales, 
+              colors, tooltips, and more.
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true

R/transcript.R

@@ -13,7 +13,7 @@
 #'
 #' @return A dataframe with the original exons and the calculated introns, sorted
 #'   by transcript and start position. Each row includes the `start`, `end`,
-#'   `type` (exon or intron), `transcript`, and `strand` for each segment.
+#'   `type` (exon, UTR or intron), `transcript`, and `strand` for each segment.
 #'
 #' @importFrom dplyr mutate filter group_by arrange lead select bind_rows
 #' @importFrom rlang .data

README.md

@@ -11,7 +11,7 @@
 
 ## geneviewer
 
-**geneviewer** is an R package for plotting gene clusters. It imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. The package offers extensive customization options, including legends, labels, annotations, scales, colors, tooltips, and more. To explore all features visit the [package website](https://nvelden.github.io/geneviewer/articles/geneviewer.html).
+**geneviewer** is an R package for plotting gene clusters and transcripts. It imports data from GenBank, FASTA, and GFF files, performs BlastP and MUMmer alignments, and displays results on gene arrow maps. The package offers extensive customization options, including legends, labels, annotations, scales, colors, tooltips, and more. To explore all features visit the [package website](https://nvelden.github.io/geneviewer/articles/geneviewer.html).
 
 ## Installation
 
@@ -54,6 +54,10 @@ For additional examples and the corresponding code to create the plots, please v
 
 <hr>
 
+<img src="man/figures/BRCA1_splice_variants.png"/>
+
+<hr>
+
 <img src="man/figures/MUMmer.png"/>
 
 <hr>

docs/articles/BLASTP_files/D3-7.8.5/lib/geneviewer-0.1.7/geneviewer.js

@@ -2565,7 +2565,7 @@ container.prototype.transcript = function (group, show = true, options = {}) {
         const { xPos, yPos, height } = getAttributesForIndex(d, i, styleIntrons, itemStyleIntrons);
         const yOffset = d.direction === 'forward' ? -height : +height;
         const rotation = this.reverse
-          ? (d.direction === 'forward' ? 180 : 0)
+          ? (d.direction === 'reverse' ? 180 : 0)
           : (d.direction === 'forward' ? 0 : 180);
         return `rotate(${rotation}, ${xPos}, ${yPos + yOffset}) translate(${xPos}, ${yPos + yOffset})`;
       })

docs/articles/BLASTP_files/Themes-0.1.7/lib/geneviewer-0.1.7/geneviewer.js

@@ -2565,7 +2565,7 @@ container.prototype.transcript = function (group, show = true, options = {}) {
         const { xPos, yPos, height } = getAttributesForIndex(d, i, styleIntrons, itemStyleIntrons);
         const yOffset = d.direction === 'forward' ? -height : +height;
         const rotation = this.reverse
-          ? (d.direction === 'forward' ? 180 : 0)
+          ? (d.direction === 'reverse' ? 180 : 0)
           : (d.direction === 'forward' ? 0 : 180);
         return `rotate(${rotation}, ${xPos}, ${yPos + yOffset}) translate(${xPos}, ${yPos + yOffset})`;
       })

docs/articles/BLASTP_files/geneviewer-0.1.7/lib/geneviewer-0.1.7/geneviewer.js

@@ -2565,7 +2565,7 @@ container.prototype.transcript = function (group, show = true, options = {}) {
         const { xPos, yPos, height } = getAttributesForIndex(d, i, styleIntrons, itemStyleIntrons);
         const yOffset = d.direction === 'forward' ? -height : +height;
         const rotation = this.reverse
-          ? (d.direction === 'forward' ? 180 : 0)
+          ? (d.direction === 'reverse' ? 180 : 0)
           : (d.direction === 'forward' ? 0 : 180);
         return `rotate(${rotation}, ${xPos}, ${yPos + yOffset}) translate(${xPos}, ${yPos + yOffset})`;
       })

docs/articles/BLASTP_files/geneviewerwidget-0.1.7/lib/geneviewer-0.1.7/geneviewer.js

@@ -2565,7 +2565,7 @@ container.prototype.transcript = function (group, show = true, options = {}) {
         const { xPos, yPos, height } = getAttributesForIndex(d, i, styleIntrons, itemStyleIntrons);
         const yOffset = d.direction === 'forward' ? -height : +height;
         const rotation = this.reverse
-          ? (d.direction === 'forward' ? 180 : 0)
+          ? (d.direction === 'reverse' ? 180 : 0)
           : (d.direction === 'forward' ? 0 : 180);
         return `rotate(${rotation}, ${xPos}, ${yPos + yOffset}) translate(${xPos}, ${yPos + yOffset})`;
       })