fix the shiny app (#15)

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: TVTB
 Type: Package
 Title: TVTB: The VCF Tool Box
-Version: 1.31.1
-Date: 2024-07-04
+Version: 1.31.2
+Date: 2024-07-05
 Authors@R: person("Kevin", "Rue-Albrecht", role = c("aut", "cre"),
     email = "[email protected]")
 Description: The package provides S4 classes and methods to filter,

inst/NEWS.Rd

@@ -1,6 +1,14 @@
 \name{TVTB-NEWS}
 \title{NEWS: The VCF Tool Box}
 
+\section{Changes in version 1.31.2 2024-07-05}{
+\subsection{Bug fix}{
+\itemize{
+\item Fix \code{tSVE()} shiny application.
+}
+}
+}
+
 \section{Changes in version 1.31.1 2024-07-04}{
 \subsection{Bug fix}{
 \itemize{

inst/extdata/SLC24A5.bed

@@ -1 +1 @@
-15  48413169    48434869    SLC24A5
+15	48413169	48434869	SLC24A5

inst/shinyApp/fileParseFunctions.R

@@ -4,7 +4,7 @@ tryParseCsq <- function(vcf, vepKey){
   message("Parsing ", vepKey," to GRanges ...")
 
   rawData <- tryCatch(
-    ensemblVEP::parseCSQToGRanges(
+    parseCSQToGRanges(
       x = vcf,
       VCFRowID = rownames(vcf),
       info.key = vepKey),

inst/shinyApp/global.R

@@ -4,7 +4,6 @@ stopifnot(
   requireNamespace("dplyr"),
   requireNamespace("DT"),
   requireNamespace("ensembldb"),
-  requireNamespace("ensemblVEP"),
   requireNamespace("ggplot2"),
   requireNamespace("reshape2"),
   requireNamespace("Rsamtools"),

inst/shinyApp/server.R

@@ -120,7 +120,7 @@ shinyServer(function(input, output, clientData, session) {
       message("Importing phenotypes ...")
       rawData <- tryCatch(
         {
-          S4Vectors::DataFrame(read.table(phenoFile, TRUE, row.names = 1))
+          S4Vectors::DataFrame(read.table(phenoFile, TRUE, row.names = 1, stringsAsFactors = TRUE))
         },
         warning = function(warn){
           Errors[["phenotypes"]] <- sprintf("Failed to parse file:\n%s", warn)
@@ -281,6 +281,7 @@ shinyServer(function(input, output, clientData, session) {
   observeEvent(
     input$phenoAddFrequencies,
     {
+      print(input$phenoAddFrequencies)
       # raw VCF
       vcf <- RV[["VCF"]]
 
@@ -289,8 +290,11 @@ shinyServer(function(input, output, clientData, session) {
 
       # phenotypes
       phenos <- SummarizedExperiment::colData(vcf)
+      print(phenos)
       phenoNames <- colnames(phenos)
+      print(phenoNames)
       phenoLevels <- levels(phenos[,input$phenoAddFrequencies])
+      print(phenoLevels)
 
       if (length(phenoLevels) == 0){
         return()
@@ -1590,10 +1594,11 @@ shinyServer(function(input, output, clientData, session) {
         RV[["VCF"]] <- NULL
         return()
       }
-
+      print(vcf)
+      print(colData(print(vcf)))
       # Clean header of INFO fields not imported
       vcf <- TVTB::dropInfo(vcf)
-
+      print(colData(print(vcf)))
       # Store ExpandedVCF object in list of reactive values
       RV[["VCF"]] <- vcf
 

inst/shinyApp/ui.R

@@ -365,13 +365,13 @@ shinyUI(navbarPage(
                 width = 2,
                 actionButton(
                   "tickAllInfo", "Select all",
-                  icon = icon("check-square-o"))
+                  icon = icon("square-check"))
               ),
               column(
                 width = 2,
                 actionButton(
                   "untickAllInfo", "Deselect all",
-                  icon = icon("square-o"))
+                  icon = icon("square"))
               ),
               column(
                 width = 7, offset = 1,
@@ -507,7 +507,7 @@ shinyUI(navbarPage(
   # Calculate frequencies ----
 
   tabPanel(
-    title = "Frequencies", icon = icon("calculator "),
+    title = "Frequencies", icon = icon("calculator"),
 
     uiOutput("TVTBparamWarning"),
 
@@ -561,13 +561,13 @@ shinyUI(navbarPage(
           actionButton(
             "tickAllPhenoLevelsFreq",
             "Select all",
-            icon = icon("check-square-o"),
+            icon = icon("square-check"),
             width = "100%"
           ), br(),
           actionButton(
             "untickAllPhenoLevelsFreq",
             "Deselect all",
-            icon = icon("square-o"),
+            icon = icon("square"),
             width = "100%"
           )
         ),
@@ -731,7 +731,7 @@ shinyUI(navbarPage(
   ),
 
   tabPanel(
-    title = "Views", icon = icon("picture-o"),
+    title = "Views", icon = icon("image"),
 
     tabsetPanel(
       id = "tabset.views",
@@ -895,7 +895,7 @@ shinyUI(navbarPage(
               "to generate/update the figure",
               actionButton(
                 "doGenoHeatmap", "Go!",
-                icon = icon("time")
+                icon = icon("hourglass-start")
               )
             ),