1. GSVA
  2. inst
  3. shinyApp
  4. geneSetsModule.R
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Updated vignette, documentation and NEWS file, corrected some messages and warnings.

Robert Castelo authored on 18/05/2021 21:31:15
Showing 1 changed files
inst/shinyApp/geneSetsModule.R
History View file @ a795b9e4
... ... 
@@ -7,12 +7,12 @@ geneSetsUI <- function(id){
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                    "From workspace" = "varGeneset")),
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     conditionalPanel(
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       condition = "input.genesetSourceType == 'fileGeneset'", ns = ns,
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-      fileInput(ns("genesetFile"), "Choose GeneSet file:",
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+      fileInput(ns("genesetFile"), "Choose gene sets file:",
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                 accept = c(".gmt", "text/csv", ".csv"))
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     ),
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     conditionalPanel(
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       condition = "input.genesetSourceType == 'varGeneset'", ns = ns,
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-      selectInput(ns("genesetVar"), "Choose GeneSet var:",
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+      selectInput(ns("genesetVar"), "Choose gene sets object:",
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                   ls(envir=.GlobalEnv))
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     )
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   )
... ... 
@@ -42,4 +42,4 @@ geneSetsServer <- function(id){
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       }
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     })
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   })
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-}
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\ No newline at end of file
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+}
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new css changes in dashboard

pablo-rodr-bio2 authored on 17/05/2021 17:29:04
Showing 1 changed files
inst/shinyApp/geneSetsModule.R
History View file @ f30da782
... ... 
@@ -1,8 +1,9 @@
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 geneSetsUI <- function(id){
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   ns <- NS(id)
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   div( id = ns("genesets-input"),
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-    radioButtons(ns("genesetSourceType"), "Select Gene Sets:",
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-                 c("From file" = "fileGeneset",
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+    radioButtons(ns("genesetSourceType"),
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+                 label = h5("GENE SETS", style="font-weight: bold"),
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+                 choices = c("From file" = "fileGeneset",
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                    "From workspace" = "varGeneset")),
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     conditionalPanel(
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       condition = "input.genesetSourceType == 'fileGeneset'", ns = ns,
Browse code

beautifying UI

pablo-rodr-bio2 authored on 14/05/2021 09:37:52
Showing 1 changed files
inst/shinyApp/geneSetsModule.R
History View file @ 282aaa63
... ... 
@@ -1,7 +1,7 @@
1 1 
 geneSetsUI <- function(id){
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   ns <- NS(id)
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-  tagList(
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-    radioButtons(ns("genesetSourceType"), "Select gene sets:",
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+  div( id = ns("genesets-input"),
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+    radioButtons(ns("genesetSourceType"), "Select Gene Sets:",
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                  c("From file" = "fileGeneset",
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                    "From workspace" = "varGeneset")),
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     conditionalPanel(
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added shinytest

pablo-rodr-bio2 authored on 23/04/2021 10:14:15
Showing 1 changed files
inst/shinyApp/geneSetsModule.R
History View file @ 30597d38
... ... 
@@ -7,7 +7,7 @@ geneSetsUI <- function(id){
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     conditionalPanel(
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       condition = "input.genesetSourceType == 'fileGeneset'", ns = ns,
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       fileInput(ns("genesetFile"), "Choose GeneSet file:",
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-                accept = ".gmt")
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+                accept = c(".gmt", "text/csv", ".csv"))
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     ),
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     conditionalPanel(
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       condition = "input.genesetSourceType == 'varGeneset'", ns = ns,
... ... 
@@ -22,7 +22,12 @@ geneSetsServer <- function(id){
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     geneSets <- reactive({
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       if(input$genesetSourceType == "fileGeneset"){
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         if(is.null(input$genesetFile)) return(NULL) #this is in order to disable "run" btn
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-        genesets <- getGmt(input$genesetFile$datapath)
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+        ext <- tools::file_ext(input$genesetFile$name)
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+        genesets <-
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+          switch(ext,
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+                 csv = as.list(read.csv(input$genesetFile$datapath)),
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+                 gmt = getGmt(input$genesetFile$datapath)
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+        )
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       } else {
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         if(is.null(input$genesetVar)) return(NULL)
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         genesets <- get(input$genesetVar)
Browse code

adding comments to code

pablo-rodr-bio2 authored on 20/04/2021 13:46:22
Showing 1 changed files
inst/shinyApp/geneSetsModule.R
History View file @ 81a33b3a
... ... 
@@ -21,7 +21,7 @@ geneSetsServer <- function(id){
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   moduleServer( id, function(input, output, session){
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     geneSets <- reactive({
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       if(input$genesetSourceType == "fileGeneset"){
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-        if(is.null(input$genesetFile)) return(NULL)
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+        if(is.null(input$genesetFile)) return(NULL) #this is in order to disable "run" btn
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         genesets <- getGmt(input$genesetFile$datapath)
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       } else {
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         if(is.null(input$genesetVar)) return(NULL)
Browse code

modules in shinyApp

pablo-rodr-bio2 authored on 12/04/2021 19:41:34
Showing 1 changed files
inst/shinyApp/geneSetsModule.R
History View file @ ca2b622a
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new file mode 100644
... ... 
@@ -0,0 +1,39 @@
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+geneSetsUI <- function(id){
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+  ns <- NS(id)
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+  tagList(
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+    radioButtons(ns("genesetSourceType"), "Select gene sets:",
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+                 c("From file" = "fileGeneset",
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+                   "From workspace" = "varGeneset")),
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+    conditionalPanel(
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+      condition = "input.genesetSourceType == 'fileGeneset'", ns = ns,
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+      fileInput(ns("genesetFile"), "Choose GeneSet file:",
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+                accept = ".gmt")
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+    ),
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+    conditionalPanel(
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+      condition = "input.genesetSourceType == 'varGeneset'", ns = ns,
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+      selectInput(ns("genesetVar"), "Choose GeneSet var:",
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+                  ls(envir=.GlobalEnv))
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+    )
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+  )
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+}
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+
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+geneSetsServer <- function(id){
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+  moduleServer( id, function(input, output, session){
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+    geneSets <- reactive({
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+      if(input$genesetSourceType == "fileGeneset"){
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+        if(is.null(input$genesetFile)) return(NULL)
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+        genesets <- getGmt(input$genesetFile$datapath)
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+      } else {
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+        if(is.null(input$genesetVar)) return(NULL)
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+        genesets <- get(input$genesetVar)
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+      }
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+      genesets
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+    }) %>% bindCache({
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+      if(input$genesetSourceType == "fileGeneset"){
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+        input$genesetFile$name
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+      } else {
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+        input$genesetVar
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+      }
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+    })
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+  })
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+}
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