@@ -12,7 +12,7 @@ Imports: methods, stats, utils, graphics, S4Vectors, IRanges,

          DelayedMatrixStats, HDF5Array, BiocSingular

 Suggests: BiocGenerics, RUnit, BiocStyle, knitr, markdown, limma, RColorBrewer,

           genefilter, edgeR, GSVAdata, shiny, shinythemes, ggplot2, data.table,

-          plotly, shinyjs, future, promises, shinybusy

+          plotly, shinyjs, future, promises, shinybusy, org.Hs.eg.db

 Description: Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.

 License: GPL (>= 2)

 VignetteBuilder: knitr

@@ -1,10 +1,11 @@

 igsva <- function() {

   shinydeps <- c("shiny", "shinythemes", "ggplot2",

-                 "data.table", "plotly")

+                 "data.table", "plotly", "future",

+                 "shinyjs", "shinybusy")

   maskshinydeps <- shinydeps %in% installed.packages()

   if (any(!maskshinydeps))

-    stop(sprintf("Please install the following packages to use the GenomiScores WebApp:\n\n  %s\n",

+    stop(sprintf("Please install the following packages to use the GSVA WebApp:\n\n  %s\n",

                  paste(shinydeps[!maskshinydeps], collapse=", ")))

   namespaceImportFrom(self=getNamespace("base"),

@@ -25,6 +26,15 @@ igsva <- function() {

   namespaceImportFrom(self=getNamespace("base"),

                       ns=getNamespace("plotly"),

                       vars=c("ggplotly", "event_data", "style"))

+  

+  namespaceImportFrom(self=getNamespace("base"),

+                      ns=getNamespace("future"))

+  

+  namespaceImportFrom(self=getNamespace("base"),

+                      ns=getNamespace("shinyjs"))

+  

+  namespaceImportFrom(self=getNamespace("base"),

+                      ns=getNamespace("shinybusy"))

   appDir <- system.file("shinyApp", package="GSVA")

   if (appDir == "")

new file mode 100644

@@ -0,0 +1,24 @@

+closeBtnUI <- function(id){

+  ns <- NS(id)

+  hidden(actionButton(ns("closeSave"), "Save & Close"))

+}

+

+closeBtnServer <- function(id, gs){

+  moduleServer(

+    id, 

+    function(input, output, session){

+      # SAVE & CLOSE BTN

+      observe({

+        if(is.null(gs())){

+          hide("closeSave")

+        } else {

+          show("closeSave")

+        }

+      })

+      

+      observeEvent(input$closeSave, {

+        stopApp(gs()) #Stops the app and returns the rv$gs object to the R session

+      })

+    }

+  )

+}

\ No newline at end of file

@@ -1,9 +1,6 @@

 downloadUI <- function(id) {

   ns <- NS(id)

-  tagList(

-    downloadButton(ns('downloadData'), 'Download'),

-    actionButton(ns('closeSave'),'Save & Close')

-  )

+  hidden(downloadButton(ns('downloadData'), 'Download'))

 }

 downloadServer <- function(id, gs){

@@ -11,6 +8,11 @@ downloadServer <- function(id, gs){

     id,

     function(input, output, session){

       #Controls the Download button

+      

+      observe({

+        

+      })

+      

       output$downloadData <- downloadHandler(

         filename = function() {

           paste("gsva_es-", Sys.Date(), ".csv", sep="")

@@ -19,4 +19,5 @@ source("plot2_Module.R")

 source("plot3_Module.R")

 source("matrixModule.R")

 source("geneSetsModule.R")

-source("argumentsDataModule.R")

\ No newline at end of file

+source("argumentsDataModule.R")

+source("closeModule.R")

\ No newline at end of file

@@ -111,14 +111,12 @@ function(input, output, session) {

     ind <- ind$pointNumber+1

   })

   plot3_Server("plot3", eventData2, rv, rv$matrix, rv$genesets)

-

-  # SAVE & CLOSE BTN

-  observeEvent(input$closeSave, {

-    stopApp(rv$gs) #Stops the app and returns the rv$gs object to the R session

-  })

   # DWN BTN

   downloadServer("download", rv$gs)

+  

+  # CLOSE BTN

+  closeBtnServer("close", reactive(rv$gs))

   # TEXT1

@@ -39,7 +39,8 @@ fluidPage(

                                    htmlOutput("text1"),

                                    plot1_UI("plot1"),

                                    tableOutput("result"),

-                                   downloadUI("download")),

+                                   downloadUI("download"),

+                                   closeBtnUI("close")),

                           tabPanel("Gene Sets",

                                    uiOutput("text2"),

                                    htmlOutput("text3"),