(up) upload app with real data

README.md

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 # samples_archive
-Archive with samples data available and doctor information
+Data archive with samples data available and doctor information
+
+https://uclanelsonlab.github.io/samples_archive/

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+}

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ccrd/.Rproj.user/F8997808/sources/per/t/AA777CF8-contents

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+#
+# This is a Shiny web application. You can run the application by clicking
+# the 'Run App' button above.
+#
+# Find out more about building applications with Shiny here:
+#
+#    http://shiny.rstudio.com/
+#
+
+library(shiny)
+library(readxl);
+
+path <- 'data/2024-06-11_UDN-Gateway_families.xlsx';
+excel_sheets(path = path);
+data <- read_excel(path = path, sheet = '2024-06-11_UDN-Gateway_families');
+data <- data[data$Status %in% c('Solved - KP', 'Solved - ND', 'Solved - PE', 'Unsolved - CG', 'Unsolved - CS'),];
+colnames(data)[2] <- 'Cases';
+colnames(data)[14] <- 'gene.of.interest';
+data <- data[!is.na(data$gene.of.interest),];
+data$referred.by <- paste(data$`Referring physician`, data$`Referring institution`, sep = '|');
+
+# data.participants <- data.frame(UDN.id = rep(NA,3), relationship = c('Proband', 'Father', 'Mother'), affected = c('Yes', 'No', 'No'), available = c('Yes', 'Yes', 'Yes'));
+path <- 'data/main.xlsx';
+excel_sheets(path = path)
+data.participants <- read_excel(path = path, sheet = 'participant');
+data.participants <- merge(x = data, y = data.participants, by.x = 'Cases', by.y = 'family_id*');
+colnames(data.participants)[29] <- 'Participants';
+colnames(data.participants)[39] <- 'Relationship';
+colnames(data.participants)[47] <- 'Affected?';
+colnames(data.participants)[4] <- 'Available?';
+data.participants[!is.na(data.participants[,4]),4] <- 'No';
+data.participants[is.na(data.participants[,4]),4] <- 'Yes';
+
+path <- 'data/main.xlsx';
+excel_sheets(path = path)
+data.analyte <- read_excel(path = path, sheet = 'analyte');
+data.analyte <- merge(x = data.participants, y = data.analyte, by.x = 'Participants', by.y = 'participant_id*');
+
+# Define UI for application that draws a histogram
+ui <- fluidPage(
+
+  # Application title
+  titlePanel("California Center for Rare Diseases"),
+
+  # Sidebar with a slider input for number of bins 
+  # sidebarLayout(
+  #   sidebarPanel = sidebarPanel(
+  textInput(inputId = 'gene', label = 'Gene name: ', value = 'RBBP5', width = '400px', placeholder = 'RBBP5'),
+  # actionButton(inputId = 'search', label = 'Search', icon = NULL, width = '400px', disabled = FALSE),
+  #   ),
+  # mainPanel = mainPanel(
+  tableOutput(outputId = 'cases'),
+  tableOutput(outputId = 'participants'),
+  tableOutput(outputId = 'biospecimens'),
+  'E: Whole Exome Sequencing; G: Whole Genome Sequencing; R: RNA-Seq'
+  #     )
+  # )
+);
+
+# Define server logic required to draw a histogram
+server <- function(input, output) {
+  output$cases <- renderTable(expr = {
+    if(!is.null(x = input$gene)){
+      return(data[data$gene.of.interest == input$gene,c('Cases', 'Status', 'referred.by')]);
+    }
+    return(data,c('Cases', 'Status', 'referred.by'));
+  });
+  output$participants <- renderTable(expr = {
+    if(!is.null(x = input$gene)){
+      return(data.participants[data.participants$gene.of.interest == input$gene,c('Participants', 'Relationship', 'Affected?', 'Available?')]);
+    }
+    return(data.participants[,c('Participants', 'Relationship', 'Affected?', 'Available?')])
+  });
+  output$biospecimens <- renderTable(expr = {
+    .data.analyte <- data.analyte[data.analyte$gene.of.interest == input$gene,];
+    Biospecimens <- unique(sort(data.analyte$`primary_biosample*`));
+    collected.P <- c(
+      ifelse(test = sum(.data.analyte$Relationship == 'Self' & .data.analyte$`primary_biosample*` == Biospecimens[1], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Self' & .data.analyte$`primary_biosample*` == Biospecimens[2], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Self' & .data.analyte$`primary_biosample*` == Biospecimens[3], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Self' & .data.analyte$`primary_biosample*` == Biospecimens[4], na.rm = TRUE) > 0, yes = 'Yes', no = 'No')
+    );
+    collected.F <- c(
+      ifelse(test = sum(.data.analyte$Relationship == 'Father' & .data.analyte$`primary_biosample*` == Biospecimens[1], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Father' & .data.analyte$`primary_biosample*` == Biospecimens[2], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Father' & .data.analyte$`primary_biosample*` == Biospecimens[3], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Father' & .data.analyte$`primary_biosample*` == Biospecimens[4], na.rm = TRUE) > 0, yes = 'Yes', no = 'No')
+    );
+    collected.M <- c(
+      ifelse(test = sum(.data.analyte$Relationship == 'Mother' & .data.analyte$`primary_biosample*` == Biospecimens[1], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Mother' & .data.analyte$`primary_biosample*` == Biospecimens[2], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Mother' & .data.analyte$`primary_biosample*` == Biospecimens[3], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Mother' & .data.analyte$`primary_biosample*` == Biospecimens[4], na.rm = TRUE) > 0, yes = 'Yes', no = 'No')
+    );
+    available.P <- rep('?', 4);
+    available.F <- rep('?', 4);
+    available.M <- rep('?', 4);
+    sequencing.P <- c('R', 'X', 'G', 'R');
+    sequencing.F <- c('X', 'X', 'G', 'X');
+    sequencing.M <- c('X', 'X', 'G', 'X');
+    contact <- c('CCRD', 'CCRD', 'CCRD', 'CDMD');
+    data.biospecimens <- data.frame(
+      Biospecimens, rep('',4), collected.P, collected.F, collected.M, rep('',4), available.P,
+      available.F, available.M, rep('',4), sequencing.P, sequencing.F, sequencing.M, contact);
+    colnames(data.biospecimens) <- c(
+      'Biospecimens', 'Collected?', 'P', 'F', 'M', 'Available?', 'P', 'F', 'M', 'Sequenced?', 'P',
+      'F', 'M', 'Contact');
+    return(data.biospecimens);
+  });
+}
+
+# Run the application 
+shinyApp(ui = ui, server = server)

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+~%2FDocuments%2Fnelson-lab%2FR-projects%2Fccrd%2Fapp.R="BBFAB3DA"
+~%2FDocuments%2Fnelson-lab%2FR-projects%2Fccrd%2Fapp2%2Fapp.R="35D8C3F2"

ccrd/.Rproj.user/shared/notebooks/paths

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+/Users/rcoronadelafuente/Documents/nelson-lab/R-projects/ccrd/app2/app.R="4749D6BA"

ccrd/app.R

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+#
+# This is a Shiny web application. You can run the application by clicking
+# the 'Run App' button above.
+#
+# Find out more about building applications with Shiny here:
+#
+#    http://shiny.rstudio.com/
+#
+
+library(shiny)
+library(readxl);
+
+path <- 'data/2024-06-11_UDN-Gateway_families_filter.xlsx';
+excel_sheets(path = path);
+data <- read_excel(path = path, sheet = '2024-06-11_UDN-Gateway_families');
+data <- data[data$Status %in% c('Solved - KP', 'Solved - ND', 'Solved - PE', 'Unsolved - CG', 'Unsolved - CS'),];
+colnames(data)[colnames(data) %in% c("primaryRelative.udnId")] <- 'Cases';
+colnames(data)[colnames(data) %in% c("List of Genes\r\n(red = NOT in Gateway)")] <- 'gene.of.interest';
+data <- data[!is.na(data$gene.of.interest),];
+data$referred.by <- paste(data$'Referring physician', data$'Referring institution', sep = '|');
+
+# data.participants <- data.frame(UDN.id = rep(NA,3), relationship = c('Proband', 'Father', 'Mother'), affected = c('Yes', 'No', 'No'), available = c('Yes', 'Yes', 'Yes'));
+path <- 'data/main.xlsx';
+excel_sheets(path = path)
+data.participants <- read_excel(path = path, sheet = 'participant');
+data.participants <- merge(x = data, y = data.participants, by.x = 'Cases', by.y = 'family_id*');
+colnames(data.participants)[colnames(data.participants) %in% c("participant_id*")] <- 'Participants';
+colnames(data.participants)[colnames(data.participants) %in% c("proband_relationship*")] <- 'Relationship';
+colnames(data.participants)[colnames(data.participants) %in% c("affected_status*")] <- 'Affected?';
+colnames(data.participants)[colnames(data.participants) %in% c("Deceased")] <- 'Available?';
+data.participants[!is.na(data.participants$"Available?"),"Available?"] <- 'No';
+data.participants[is.na(data.participants$"Available?"),"Available?"] <- 'Yes';
+
+path <- 'data/main.xlsx';
+excel_sheets(path = path)
+data.analyte <- read_excel(path = path, sheet = 'analyte');
+data.analyte <- merge(x = data.participants, y = data.analyte, by.x = 'Participants', by.y = 'participant_id*');
+
+# Define UI for application that draws a histogram
+ui <- fluidPage(
+
+  # Application title
+  titlePanel("California Center for Rare Diseases"),
+
+  # Sidebar with a slider input for number of bins 
+  # sidebarLayout(
+  #   sidebarPanel = sidebarPanel(
+  textInput(inputId = 'gene', label = 'Gene name: ', value = 'RBBP5', width = '400px', placeholder = 'RBBP5'),
+  # actionButton(inputId = 'search', label = 'Search', icon = NULL, width = '400px', disabled = FALSE),
+  #   ),
+  # mainPanel = mainPanel(
+  tableOutput(outputId = 'cases'),
+  tableOutput(outputId = 'participants'),
+  tableOutput(outputId = 'biospecimens'),
+  'E: Whole Exome Sequencing; G: Whole Genome Sequencing; R: RNA-Seq'
+  #     )
+  # )
+);
+
+# Define server logic required to draw a histogram
+server <- function(input, output) {
+  output$cases <- renderTable(expr = {
+    if(!is.null(x = input$gene)){
+      return(data[data$gene.of.interest == input$gene,c('Cases', 'Status', 'referred.by')]);
+    }
+    return(data,c('Cases', 'Status', 'referred.by'));
+  });
+  output$participants <- renderTable(expr = {
+    if(!is.null(x = input$gene)){
+      return(data.participants[data.participants$gene.of.interest == input$gene,c('Participants', 'Relationship', 'Affected?', 'Available?')]);
+    }
+    return(data.participants[,c('Participants', 'Relationship', 'Affected?', 'Available?')])
+  });
+  output$biospecimens <- renderTable(expr = {
+    .data.analyte <- data.analyte[data.analyte$gene.of.interest == input$gene,];
+    Biospecimens <- unique(sort(data.analyte$`primary_biosample*`));
+    collected.P <- c(
+      ifelse(test = sum(.data.analyte$Relationship == 'Self' & .data.analyte$`primary_biosample*` == Biospecimens[1], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Self' & .data.analyte$`primary_biosample*` == Biospecimens[2], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Self' & .data.analyte$`primary_biosample*` == Biospecimens[3], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Self' & .data.analyte$`primary_biosample*` == Biospecimens[4], na.rm = TRUE) > 0, yes = 'Yes', no = 'No')
+    );
+    collected.F <- c(
+      ifelse(test = sum(.data.analyte$Relationship == 'Father' & .data.analyte$`primary_biosample*` == Biospecimens[1], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Father' & .data.analyte$`primary_biosample*` == Biospecimens[2], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Father' & .data.analyte$`primary_biosample*` == Biospecimens[3], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Father' & .data.analyte$`primary_biosample*` == Biospecimens[4], na.rm = TRUE) > 0, yes = 'Yes', no = 'No')
+    );
+    collected.M <- c(
+      ifelse(test = sum(.data.analyte$Relationship == 'Mother' & .data.analyte$`primary_biosample*` == Biospecimens[1], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Mother' & .data.analyte$`primary_biosample*` == Biospecimens[2], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Mother' & .data.analyte$`primary_biosample*` == Biospecimens[3], na.rm = TRUE) > 0, yes = 'Yes', no = 'No'),
+      ifelse(test = sum(.data.analyte$Relationship == 'Mother' & .data.analyte$`primary_biosample*` == Biospecimens[4], na.rm = TRUE) > 0, yes = 'Yes', no = 'No')
+    );
+    available.P <- rep('?', 4);
+    available.F <- rep('?', 4);
+    available.M <- rep('?', 4);
+    sequencing.P <- c('R', 'X', 'G', 'R');
+    sequencing.F <- c('X', 'X', 'G', 'X');
+    sequencing.M <- c('X', 'X', 'G', 'X');
+    contact <- c('CCRD', 'CCRD', 'CCRD', 'CDMD');
+    data.biospecimens <- data.frame(
+      Biospecimens, rep('',4), collected.P, collected.F, collected.M, rep('',4), available.P,
+      available.F, available.M, rep('',4), sequencing.P, sequencing.F, sequencing.M, contact);
+    colnames(data.biospecimens) <- c(
+      'Biospecimens', 'Collected?', 'P', 'F', 'M', 'Available?', 'P', 'F', 'M', 'Sequenced?', 'P',
+      'F', 'M', 'Contact');
+    return(data.biospecimens);
+  });
+}
+
+# Run the application 
+shinyApp(ui = ui, server = server)

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