Merge pull request #15 from allaway/gene_var_1

adding some user friendly declarations!
nf-osi · Jan 29, 2020 · 080fbf3 · 080fbf3
2 parents 7640d1d + e4bb74e
commit 080fbf3
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Showing 2 changed files with 28 additions and 4 deletions.
diff --git a/R/mod_gene_var.R b/R/mod_gene_var.R
@@ -25,12 +25,17 @@ mod_gene_variant_ui <- function(id){
       selectizeInput(ns("Genes"), label = "Genes", choices = unique(kairos::jhu_tumor_file@data$Hugo_Symbol),
                      selected = "NF1", multiple = F),
 
+      box(title = "Samples in the selected cohort", 
+          status = "primary", solidHeader = TRUE,
+          width = 1000,
+          collapsible = FALSE,
+          textOutput(ns('sample_check'))),
+
       box(title = "Positional information of variants in tumor samples", 
           status = "primary", solidHeader = TRUE,
           width = 1000,
           collapsible = FALSE,
-          plotOutput(ns('lollipop_plot'))
-      )
+          plotOutput(ns('lollipop_plot')))
 
     )
   )
@@ -45,15 +50,33 @@ mod_gene_variant_ui <- function(id){
 mod_gene_variant_server <- function(input, output, session, specimens){
   ns <- session$ns
 
+  output$sample_check <- shiny::renderText({
+
+    tumor_sample_bc <- as.vector(kairos::jhu_tumor_file@data$Tumor_Sample_Barcode[kairos::jhu_tumor_file@clinical.data$specimenID %in% 
+                                                                                    specimens()])
+
+      if(length(tumor_sample_bc)>0) {
+      file_with_specimen <- maftools::subsetMaf(kairos::jhu_tumor_file, tsb = c(tumor_sample_bc))
+      base::ifelse(all(specimens() %in% file_with_specimen@clinical.data$specimenID),
+                   "All samples in your selected cohort have genomic variant data. They are plotted below",
+                   "Only a subset of selected cohort has genomic variant data. They are plotted below.")
+    } else(
+      print("No variant data found. Please modify your cohort.")
+    )
+
+  })
+
   output$lollipop_plot <- shiny::renderPlot({
 
     tumor_sample_bc <- as.vector(kairos::jhu_tumor_file@data$Tumor_Sample_Barcode[kairos::jhu_tumor_file@clinical.data$specimenID %in% specimens()])
+
     validate(need(length(tumor_sample_bc)>0, "No variant data found. Please modify your cohort."))
-
+    
     file_with_specimen <- maftools::subsetMaf(kairos::jhu_tumor_file, tsb = c(tumor_sample_bc))
+
 
     maftools::lollipopPlot(
-      kairos::jhu_tumor_file,
+      file_with_specimen,
       gene = input$Genes,
       AACol = NULL,
       labelPos = NULL,

diff --git a/dev/run_dev.R b/dev/run_dev.R
@@ -11,3 +11,4 @@ golem::document_and_reload()
 # Run the application
 kairos::run_app()
 
+
Original file line number	Diff line number	Diff line change
Expand Up		@@ -11,3 +11,4 @@ golem::document_and_reload()
		# Run the application
		kairos::run_app()