Gene Variant Module

NAMESPACE

@@ -9,6 +9,8 @@ export(mod_docs_page_server)
 export(mod_docs_page_ui)
 export(mod_explore_page_server)
 export(mod_explore_page_ui)
+export(mod_gene_variant_server)
+export(mod_gene_variant_ui)
 export(mod_latent_variables_server)
 export(mod_latent_variables_ui)
 export(mod_resources_page_server)

R/mod_explore_page.R

@@ -31,6 +31,11 @@ mod_explore_page_ui <- function(id){
                      tabName = "immune_infiltration",
                      icon = icon("cog")
                    ),
+                   menuSubItem(
+                     "Gene Variants",
+                     tabName = "gene_var",
+                     icon = icon("cog")
+                   ),
                    menuSubItem(
                      "Latent Variables",
                      tabName = "latent_variables",
@@ -44,6 +49,10 @@ mod_explore_page_ui <- function(id){
               tabItem(
                 tabName = 'immune_infiltration'
                 ),
+              tabItem(
+                tabName = "gene_var",
+                mod_gene_variant_ui(ns("gene_variant_ui"))
+              ),
               tabItem(
                 tabName = "latent_variables",
                 mod_latent_variables_ui(ns("latent_variables_ui_1"))
@@ -63,6 +72,7 @@ mod_explore_page_ui <- function(id){
 mod_explore_page_server <- function(input, output, session, specimens){
   ns <- session$ns
 
+  callModule(mod_gene_variant_server, "gene_variant_ui")
   callModule(mod_latent_variables_server, "latent_variables_ui_1", specimens)  
 }
 

R/mod_gene_var.R

@@ -0,0 +1,93 @@
+# Module UI
+
+#' @title   mod_gene_variant_ui and mod_gene_variant_server
+#' @description  A shiny Module.
+#'
+#' @param id shiny id
+#' @param input internal
+#' @param output internal
+#' @param session internal
+#'
+#' @rdname mod_gene_variant
+#'
+#' @keywords internal
+#' @export 
+#' @importFrom shiny NS tagList 
+mod_gene_variant_ui <- function(id){
+  ns <- NS(id)
+
+  dashboardBody(
+    tagList(
+
+      # selectizeInput(ns("studyName"), label = "Study Name", choices = unique(kairos::exome_data$study),
+      #                selected = unique(kairos::exome_data$study), multiple = T),
+      # 
+      selectizeInput(ns("Genes"), label = "Genes", choices = unique(kairos::jhu_tumor_file@data$Hugo_Symbol),
+                     selected = "NF1", multiple = F),
+
+      box(title = "Positional information of variants in tumor samples", 
+          status = "primary", solidHeader = TRUE,
+          width = 1000,
+          collapsible = FALSE,
+          plotOutput(ns('lollipop_plot'))
+      )
+
+    )
+  )
+}
+
+# Module Server
+
+#' @rdname mod_gene_variant
+#' @export
+#' @keywords internal
+
+mod_gene_variant_server <- function(input, output, session){
+  ns <- session$ns
+
+  output$lollipop_plot <- shiny::renderPlot({
+
+    maftools::lollipopPlot(
+      kairos::jhu_tumor_file,
+      gene = input$Genes,
+      AACol = NULL,
+      labelPos = NULL,
+      labPosSize = 0.9,
+      showMutationRate = TRUE,
+      showDomainLabel = TRUE,
+      cBioPortal = FALSE,
+      refSeqID = NULL,
+      proteinID = NULL,
+      repel = FALSE,
+      collapsePosLabel = TRUE,
+      legendTxtSize = 1.5,
+      labPosAngle = 0,
+      domainLabelSize = 1.5,
+      axisTextSize = c(1, 1),
+      printCount = FALSE,
+      colors = NULL,
+      domainColors = NULL,
+      labelOnlyUniqueDoamins = TRUE,
+      defaultYaxis = FALSE,
+      titleSize = c(1.2, 1),
+      pointSize = 2.5
+    )
+
+    # maftools::oncoplot(kairos::jhu_tumor_file, 
+    #                    genes = c("NF1", "EGR2"),
+    #                    drawRowBar = TRUE, drawColBar = TRUE,
+    #                    clinicalFeatures = c("tumorType", "sampleType","individualID"),
+    #                    #sortByAnnotation = TRUE, annotationColor = color_list, groupAnnotationBySize = FALSE, 
+    #                    removeNonMutated = FALSE, logColBar = FALSE,
+    #                    SampleNamefont = 5,annotationFontSize = 1.5, fontSize = 1,legendFontSize = 1.8,
+    #                    titleFontSize = 1.0, keepGeneOrder = TRUE, GeneOrderSort = TRUE, bgCol = "white", borderCol = "white")
+  })
+
+}
+
+## To be copied in the UI
+# mod_gene_variant_ui("gene_variant_ui")
+
+## To be copied in the server
+# callModule(mod_gene_variant_server, "gene_variant_ui")
+

data-raw/jhu_maf.R

@@ -0,0 +1,3 @@
+#Prep Maf file for plotting
+load("data-raw/jhu_maf.RData")
+usethis::use_data(jhu_tumor_file)