fix shiny app

kevinrue · Jul 6, 2024 · 73c3c2e · 73c3c2e
1 parent 1d26c4b
commit 73c3c2e
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Showing 4 changed files with 9 additions and 10 deletions.
diff --git a/inst/shinyApp/fileParseFunctions.R b/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),

diff --git a/inst/shinyApp/global.R b/inst/shinyApp/global.R
@@ -3,7 +3,6 @@ stopifnot(
   requireNamespace("BiocParallel"),
   requireNamespace("dplyr"),
   requireNamespace("DT"),
-  requireNamespace("ensembldb"),
   requireNamespace("ensemblVEP"),
   requireNamespace("ggplot2"),
   requireNamespace("reshape2"),

diff --git a/inst/shinyApp/server.R b/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)

diff --git a/inst/shinyApp/ui.R b/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")
               )
             ),