@@ -188,17 +188,20 @@ function(input, output, session) {

     req(rv$gs)

     tagList(

       br(),

-      div("To see the Empirical Cumulative Distribution Function 

-      of a Sample, click on its line in this plot and go to the 

-      'Gene.Set' Panel", style="text-align: center;")

+      div("Non-parametric kernel density estimation of sample

+          profiles of GSVA enrichment scores. Clicking on the

+          line of a sample will display the empirical cumulative

+          distribution of GSVA scores for that sample on the

+          'GeneSets' tab", style="text-align: center;")

     )

   })

   # TABLE

   output$result <- renderTable({

     req(rv$gs)

-    resultInformation <- data.frame("Nr of gene sets" = nrow(rv$gs),

-                                    "Nr of samples" = ncol(rv$gs))

+    resultInformation <- data.frame("Nr. of gene sets" = nrow(rv$gs),

+                                    "Nr. of samples" = ncol(rv$gs),

+                                    check.names=FALSE)

     resultInformation

   }, bordered = TRUE)

@@ -212,9 +215,11 @@ function(input, output, session) {

   output$text3 <- renderUI({

     tagList(

       br(),

-      div("To see the Kernel Density Estimation of genes of any given

-      Gene Set in this Sample,  click on any point in this plot and a

-      second plot will appear bellow it", style = "text-align: center;")

+      div("Empirical cumulative distribution of GSVA scores, where each

+          point is a gene set. Clicking on a gene set will display below

+          the individual gene expression values of its constituent genes

+          and the non-parametric kernel density estimation of their

+          distribution", style = "text-align: center;")

     )

   })

@@ -200,7 +200,7 @@ function(input, output, session) {

     resultInformation <- data.frame("Nr of gene sets" = nrow(rv$gs),

                                     "Nr of samples" = ncol(rv$gs))

     resultInformation

-  })

+  }, bordered = TRUE)

   # TEXT2

   output$text2 <- renderUI({

@@ -181,14 +181,17 @@ function(input, output, session) {

   # CLOSE BTN

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

-

+  

   # TEXT1

   output$text1 <- renderUI({

     req(rv$gs)

-    HTML(paste("<br/>", "\t To see the Empirical Cumulative Distribution Function 

-    of a Sample, click on its line in this plot and go

-      to the 'Gene.Set' Panel", "<br/>", sep="<br/>"))

+    tagList(

+      br(),

+      div("To see the Empirical Cumulative Distribution Function 

+      of a Sample, click on its line in this plot and go to the 

+      'Gene.Set' Panel", style="text-align: center;")

+    )

   })

   # TABLE

@@ -200,7 +200,7 @@ function(input, output, session) {

     resultInformation <- data.frame("Nr of gene sets" = nrow(rv$gs),

                                     "Nr of samples" = ncol(rv$gs))

     resultInformation

-  })

+  }, bordered = TRUE)

   # TEXT2

   output$text2 <- renderUI({

@@ -181,14 +181,17 @@ function(input, output, session) {

   # CLOSE BTN

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

-

+  

   # TEXT1

   output$text1 <- renderUI({

     req(rv$gs)

-    HTML(paste("<br/>", "\t To see the Empirical Cumulative Distribution Function 

-    of a Sample, click on its line in this plot and go

-      to the 'Gene.Set' Panel", "<br/>", sep="<br/>"))

+    tagList(

+      br(),

+      div("To see the Empirical Cumulative Distribution Function 

+      of a Sample, click on its line in this plot and go to the 

+      'Gene.Set' Panel", style="text-align: center;")

+    )

   })

   # TABLE

@@ -22,7 +22,8 @@ function(input, output, session) {

   ## REACTIVE VALUES

   rv <- reactiveValues(gs=NULL, dat.t=NULL, n=NULL, dd.col=NULL, p=NULL, 

-                       p2=NULL, p3=NULL, errors.gsva = NULL, sample.c = NULL)

+                       p2=NULL, p3=NULL, errors.gsva = NULL, sample.c = NULL,

+                       method=NULL)

   gsva.cancel <- reactiveVal(FALSE)

   ## GSVA RESULT

@@ -41,6 +42,7 @@ function(input, output, session) {

     rv$p3 <- NULL

     rv$sample.c <- NULL

     rv$errors.gsva <- NULL

+    rv$method <- argInp$method()

     ## this is a flag for the future. Futures cannot be canceled or

     ## terminated in a strict way, so when they get interrupted they

@@ -129,6 +129,12 @@ function(input, output, session) {

   plot2_Server("plot2", eventData1, rv)

   # PLOT3 RENDER

+  

+  ## Whenever the user clicks on the first plot, the third one resets

+  observeEvent(eventData1(), {

+    runjs("Shiny.setInputValue('plotly_click-click2', null);")

+  })

+  

   eventData2 <- reactive({

     req(rv$p2)

     ind <- event_data("plotly_click", source = "click2")

@@ -122,10 +122,9 @@ function(input, output, session) {

   # PLOT2 RENDER

   eventData1 <- reactive({

-    req(rv$dat.t)

+    if(is.null(rv$p))return(NULL)

     ind <- event_data("plotly_click", source = "click1")

     ind <- ind$curveNumber+1

-

   })

   plot2_Server("plot2", eventData1, rv)

@@ -134,7 +133,6 @@ function(input, output, session) {

     req(rv$p2)

     ind <- event_data("plotly_click", source = "click2")

     ind <- ind$pointNumber+1

-

   })

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

@@ -161,12 +159,12 @@ function(input, output, session) {

     }

   })

-  ## HIDE 'GeneSets' PANEL WHILE THERE IS NO GSVA OBJECT

+  ## HIDE 'GeneSets' PANEL WHILE THERE IS NO CLICK EVENT ON THE FIRST PLOT

   observe({

-    if(is.null(rv$gs)) {

-      hideTab(inputId="Panels", target="GeneSets")

+    if( length(eventData1()) == 0){

+      hideTab(inputId = "Panels", target = "GeneSets")

     } else {

-      showTab(inputId="Panels", target="GeneSets")

+      showTab(inputId = "Panels", target = "GeneSets", select = TRUE)

     }

   })

@@ -4,143 +4,9 @@ function(input, output, session) {

   rout <- tempfile("consoleText", fileext = ".txt")

   file.create(rout)

   console.text <- reactiveFileReader(200, session, rout, readLines, warn=F)

-<<<<<<< HEAD

-  

-  # ERRORS MESSAGES

-  output$errorsGsva <- renderText({

-    req(argInp$varMinsz(), argInp$varMaxsz(), argInp$selectedTau())

-    rv$errors.gsva

-  })

-

-  # ENABLING 'RUN' BTN

-  observe({

-    if(!is.null(matrix()) && !is.null(genesets())){

-      enable("button")

-    } else {

-      disable("button")

-    }

-  })

-  

-  ### INPUTS ###

-  

-  # DATA MATRIX

-  matrix <- matrixServer("matrix1")

-  

-  # GENES

-  genesets <- geneSetsServer("genes1")

-  

-  # ARGUMENTS

-  argInp <- argumentsDataServer("argumentsInput")

-  

-

-  #### GSVA RESULTS ####

-  

-  ## REACTIVE VALUES

-  rv <- reactiveValues(gs=NULL, dat.t=NULL, n=NULL, dd.col=NULL, p=NULL, 

-                       p2=NULL, p3=NULL, errors.gsva = NULL, sample.c = NULL)

-  gsva.cancel <- reactiveVal(FALSE)

-  

-  ## GSVA RESULT

-  observeEvent( input$button, {

-    

-    ## This js is in order to reset the event_data from the plotlys,

-    ## so every time the .user hits the 'run' button, plotlys get back to null

-    runjs("Shiny.setInputValue('plotly_click-click1', null);")

-    runjs("Shiny.setInputValue('plotly_click-click2', null);")

-    

-    ## here we reset all the reactiveValues to NULL

-    rv$gs <- NULL

-    rv$dat.t <- NULL

-    rv$p <- NULL

-    rv$p2 <- NULL

-    rv$p3 <- NULL

-    rv$sample.c <- NULL

-    rv$errors.gsva <- NULL

-    

-    ## this is a flag for the future. Futures cannot be canceled or

-    ## terminated in a strict way, so when they get interrupted they

-    ## throw an error that is not related to gsva(). When future is 

-    ## interrupted, the flag goes TRUE in order to make the errors

-    ## message print NULL

-    gsva.cancel(FALSE)

-    

-    modalGSVAUI("modal.text")

-    

-    ## future() cannot take reactive values, so we must isolate() them

-    future({

-      ## sink() will redirect all console cats and prints to a

-      ## text file that the main session will be reading in order

-      ## to print the progress bar from bplaply()

-      sink(rout)

-      result <- gsva(isolate(matrix()),

-                     isolate(genesets()), 

-                     method=isolate(argInp$method()),

-                     kcdf=isolate(argInp$kcdf()),

-                     abs.ranking=isolate(argInp$absRanking()),

-                     min.sz= isolate(argInp$varMinsz()),

-                     max.sz=isolate(argInp$varMaxsz()),

-                     parallel.sz=1L, ## by now, disable parallelism

-                     mx.diff=isolate(argInp$mxDiff()),

-                     tau=isolate(argInp$selectedTau()),

-                     ssgsea.norm=isolate(argInp$ssgseaNorm()),

-                     verbose=TRUE)

-      sink()

-      ## when gsva() ends, we reset the console text file to empty

-      write("", file=rout)

-      return(result)

-    }, seed = TRUE) %...>%

-      (function(result){

-        ## the future's result will be the gsva() result, and we save it

-        ## and transform it in reactiveValues(). In order to make the future

-        ## not block the app at an inner-session level, we save the results in

-        ## reactiveValues() and then at the end of the observeEvent() we return NULL

-        ## in order to make the plots.

-        ## https://github.com/rstudio/promises/issues/23#issuecomment-386687705

-        rv$gs <- result

-        rv$dat.t <- melt(as.data.table(rv$gs, keep.rownames = "gene.sets"),

-                         variable.name = "Sample", id.vars="gene.sets")

-        rv$n <- length(levels(rv$dat.t$Sample))

-        rv$dd.col <- hcl(h = seq(15, 375, length=rv$n), l = 65, c = 100)[1:rv$n]

-        names(rv$dd.col)  <- levels(rv$dat.t$Sample)

-        

-        ## finally, we leave the console.text file empty again and

-        ## remove the modal

-        write("", file=rout)

-        removeModal()

-      }) %...!%

-      (function(error){

-        ## there can be two ways to get an error here: 

-        ## 1. gsva() fails, which is an ok error and should be returnet to user

-        ## 2. User interrupts the future, which shouldn't be printed, that's

-        ## why I use a flag to identify if error comes from pressing "Cancel" btn

-        ## on the modal

-        removeModal()

-        write("", file=rout)

-        if(gsva.cancel()){

-          rv$errors.gsva <- NULL

-        } else {

-          rv$errors.gsva <- as.character(error)

-        }

-        

-      })

-    NULL

-  })

-  

-  # PRINTING CONSOLE.TEXT

-  modalGSVAServer("modal.text", console.text, gsva.cancel, rout)

-  

-  # PLOT1 RENDER

-  plot1_Server("plot1", rv)

-

-  # PLOT2 RENDER

-  eventData1 <- reactive({

-    req(rv$dat.t)

-    ind <- event_data("plotly_click", source = "click1")

-    ind <- ind$curveNumber+1

-=======

-  ##################### INPUTS #####################

+  ##################### INPUTS  ##################### 

   # DATA MATRIX

   matrix <- matrixServer("matrix1")

@@ -151,9 +17,8 @@ function(input, output, session) {

   # ARGUMENTS

   argInp <- argumentsDataServer("argumentsInput")

-  

-  ##################### GSVA RESULTS ################

+  ##################### GSVA RESULTS  ##################### 

   ## REACTIVE VALUES

   rv <- reactiveValues(gs=NULL, dat.t=NULL, n=NULL, dd.col=NULL, p=NULL, 

@@ -244,47 +109,12 @@ function(input, output, session) {

       })

     NULL

->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d

   })

-  plot2_Server("plot2", eventData1, rv)

-  

-<<<<<<< HEAD

-  # PLOT3 RENDER

-  eventData2 <- reactive({

-    req(rv$p2)

-    ind <- event_data("plotly_click", source = "click2")

-    ind <- ind$pointNumber+1

-  })

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

-  

-  # DWN BTN

-  downloadServer("download", reactive(rv$gs))

-  

-  # CLOSE BTN

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

-

-  

-  # TEXT1

-  output$text1 <- renderUI({

-    req(rv$gs)

-    HTML(paste("<br/>", "\t To see the Empirical Cumulative Distribution Function 

-    of a Sample, click on its line in this plot and go

-      to the 'Gene.Set' Panel", "<br/>", sep="<br/>"))

-  })

-  

-  # TABLE

-  output$result <- renderTable({

-    req(rv$gs)

-    resultInformation <- data.frame("Nr of gene sets" = nrow(rv$gs),

-                                    "Nr of samples" = ncol(rv$gs))

-    resultInformation

-=======

   # PRINTING CONSOLE.TEXT

   modalGSVAServer("modal.text", console.text, gsva.cancel, rout)

-  

   ##################### OUTPUTS ##################

   # PLOT1 RENDER

@@ -295,46 +125,29 @@ function(input, output, session) {

     req(rv$dat.t)

     ind <- event_data("plotly_click", source = "click1")

     ind <- ind$curveNumber+1

->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d

+

   })

   plot2_Server("plot2", eventData1, rv)

-  

-<<<<<<< HEAD

-  # TEXT2

-  output$text2 <- renderUI({

-    title1 <- rv$sample.c

-    h2(tags$b(title1), align ="center")

-=======

+

   # PLOT3 RENDER

   eventData2 <- reactive({

     req(rv$p2)

     ind <- event_data("plotly_click", source = "click2")

     ind <- ind$pointNumber+1

->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d

+

   })

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

-  

-<<<<<<< HEAD

-  # TEXT3

-  output$text3 <- renderUI({

-    HTML(paste("<br/>", "\t To see the Kernel Density Estimation of genes of 

-    any given Gene Set in this Sample,  click on any point in this plot and a

-    second plot will appear bellow it", "<br/>", sep="<br/>"))

-=======

+

   # ERRORS MESSAGES

   output$errorsGsva <- renderText({

     req(argInp$varMinsz(), argInp$varMaxsz(), argInp$selectedTau())

     rv$errors.gsva

->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d

   })

   # SESSION INFO

   output$sessionInfo <- renderPrint({

     sessionInfo()

   })

-<<<<<<< HEAD

-

-=======

   ##################### UI SETUPS #####################

@@ -393,6 +206,4 @@ function(input, output, session) {

     second plot will appear bellow it", "<br/>", sep="<br/>"))

   })

-

->>>>>>> 8dfc5494f0608cb5bbe03ef57fbf5f8532fe0b7d

 }

@@ -30,26 +30,46 @@ function(input, output, session) {

   # ARGUMENTS

   argInp <- argumentsDataServer("argumentsInput")

+  

   #### GSVA RESULTS ####

+  ## REACTIVE VALUES

   rv <- reactiveValues(gs=NULL, dat.t=NULL, n=NULL, dd.col=NULL, p=NULL, 

-                       errors.gsva = NULL)

+                       p2=NULL, p3=NULL, errors.gsva = NULL, sample.c = NULL)

   gsva.cancel <- reactiveVal(FALSE)

+  ## GSVA RESULT

   observeEvent( input$button, {

+    

+    ## This js is in order to reset the event_data from the plotlys,

+    ## so every time the .user hits the 'run' button, plotlys get back to null

     runjs("Shiny.setInputValue('plotly_click-click1', null);")

     runjs("Shiny.setInputValue('plotly_click-click2', null);")

+    

+    ## here we reset all the reactiveValues to NULL

     rv$gs <- NULL

     rv$dat.t <- NULL

     rv$p <- NULL

     rv$p2 <- NULL

     rv$p3 <- NULL

-    rv$errors.gsva = NULL

+    rv$sample.c <- NULL

+    rv$errors.gsva <- NULL

+    

+    ## this is a flag for the future. Futures cannot be canceled or

+    ## terminated in a strict way, so when they get interrupted they

+    ## throw an error that is not related to gsva(). When future is 

+    ## interrupted, the flag goes TRUE in order to make the errors

+    ## message print NULL

     gsva.cancel(FALSE)

+    

     modalGSVAUI("modal.text")

-    # future() cannot take reactive values, so we must isolate() them

+    

+    ## future() cannot take reactive values, so we must isolate() them

     future({

+      ## sink() will redirect all console cats and prints to a

+      ## text file that the main session will be reading in order

+      ## to print the progress bar from bplaply()

       sink(rout)

       result <- gsva(isolate(matrix()),

                      isolate(genesets()), 

@@ -64,20 +84,35 @@ function(input, output, session) {

                      ssgsea.norm=isolate(argInp$ssgseaNorm()),

                      verbose=TRUE)

       sink()

+      ## when gsva() ends, we reset the console text file to empty

       write("", file=rout)

       return(result)

     }, seed = TRUE) %...>%

       (function(result){

+        ## the future's result will be the gsva() result, and we save it

+        ## and transform it in reactiveValues(). In order to make the future

+        ## not block the app at an inner-session level, we save the results in

+        ## reactiveValues() and then at the end of the observeEvent() we return NULL

+        ## in order to make the plots.

+        ## https://github.com/rstudio/promises/issues/23#issuecomment-386687705

         rv$gs <- result

         rv$dat.t <- melt(as.data.table(rv$gs, keep.rownames = "gene.sets"),

                          variable.name = "Sample", id.vars="gene.sets")

         rv$n <- length(levels(rv$dat.t$Sample))

         rv$dd.col <- hcl(h = seq(15, 375, length=rv$n), l = 65, c = 100)[1:rv$n]

         names(rv$dd.col)  <- levels(rv$dat.t$Sample)

+        

+        ## finally, we leave the console.text file empty again and

+        ## remove the modal

         write("", file=rout)

         removeModal()

       }) %...!%

       (function(error){

+        ## there can be two ways to get an error here: 

+        ## 1. gsva() fails, which is an ok error and should be returnet to user

+        ## 2. User interrupts the future, which shouldn't be printed, that's

+        ## why I use a flag to identify if error comes from pressing "Cancel" btn

+        ## on the modal

         removeModal()

         write("", file=rout)

         if(gsva.cancel()){

@@ -111,7 +111,6 @@ function(input, output, session) {

     ind <- event_data("plotly_click", source = "click2")

     ind <- ind$pointNumber+1

   })

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

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

   # DWN BTN

@@ -34,18 +34,18 @@ function(input, output, session) {

   #### GSVA RESULTS ####

   rv <- reactiveValues(gs=NULL, dat.t=NULL, n=NULL, dd.col=NULL, p=NULL, 

-                       errors.gsva = NULL, matrix=NULL, genesets=NULL)

+                       errors.gsva = NULL)

   gsva.cancel <- reactiveVal(FALSE)

   observeEvent( input$button, {

+    runjs("Shiny.setInputValue('plotly_click-click1', null);")

+    runjs("Shiny.setInputValue('plotly_click-click2', null);")

     rv$gs <- NULL

     rv$dat.t <- NULL

     rv$p <- NULL

     rv$p2 <- NULL

     rv$p3 <- NULL

     rv$errors.gsva = NULL

-    rv$matrix <- isolate(matrix())

-    rv$genesets <- isolate(genesets())

     gsva.cancel(FALSE)

     modalGSVAUI("modal.text")

     # future() cannot take reactive values, so we must isolate() them

@@ -96,7 +96,6 @@ function(input, output, session) {

   # PLOT1 RENDER

   plot1_Server("plot1", rv)

-

   # PLOT2 RENDER

   eventData1 <- reactive({

     req(rv$dat.t)

@@ -112,7 +111,8 @@ function(input, output, session) {

     ind <- event_data("plotly_click", source = "click2")

     ind <- ind$pointNumber+1

   })

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

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

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

   # DWN BTN

   downloadServer("download", reactive(rv$gs))

@@ -41,6 +41,8 @@ function(input, output, session) {

     rv$gs <- NULL

     rv$dat.t <- NULL

     rv$p <- NULL

+    rv$p2 <- NULL

+    rv$p3 <- NULL

     rv$errors.gsva = NULL

     rv$matrix <- isolate(matrix())

     rv$genesets <- isolate(genesets())

@@ -89,7 +89,7 @@ function(input, output, session) {

   })

   # PRINTING CONSOLE.TEXT

-  modalGSVAServer("modal.text", console.text, gsva.cancel)

+  modalGSVAServer("modal.text", console.text, gsva.cancel, rout)

   # PLOT1 RENDER

   plot1_Server("plot1", rv)

@@ -113,7 +113,7 @@ function(input, output, session) {

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

   # DWN BTN

-  downloadServer("download", rv$gs)

+  downloadServer("download", reactive(rv$gs))

   # CLOSE BTN

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

@@ -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

@@ -1,361 +1,158 @@

-library(GSVA)

-library(shiny)

-library(shinythemes)

-library(GSEABase)

-library(GSVAdata)

-library(limma)

-library(ggplot2)

-library(data.table)

-library(plotly)

-

-argumentsDataInput <- function(id) {

-  # Create a namespace function using the provided id

-  ns <- NS(id)

+function(input, output, session) {

-  #UI Definition

-  column(

-    3,

-    conditionalPanel(

-      condition = "input.arg == 'yes'",

-      h3("Select arguments:"),

-      wellPanel(fluidRow(

-        column(

-          12,

-          selectInput("method", "Choose method:",

-                      c("gsva","ssgsea","zscore","plage")),

-          selectInput("kcdf", "Choose kcdf:",

-                      c("Gaussian","Poisson","none")),

-          radioButtons("absRanking", "abs.ranking:",

-                       c("False" = FALSE,

-                         "True" = TRUE)),

-          numericInput("minSz","min.sz:",value = 1),

-          numericInput("maxSz","max.sz (Write 0 for infinite):",value = 0),

-          ## numericInput("parallelSz","parallel.sz:",value = 0),

-          ## selectInput("parallelType", "parallel.type:",

-          ##             c("SOCK","MPI","NWS")),

-          radioButtons("mxDiff", "mx.diff:",

-                       c("True" = TRUE,

-                         "False" = FALSE)),

-          conditionalPanel(

-            condition = "input.method == 'gsva'",

-            numericInput("tau1","tau:",value = 1)

-          ),

-          conditionalPanel(

-            condition = "input.method == 'ssgsea'",

-            numericInput("tau2","tau:",value = 0.25)

-          ),

-          conditionalPanel(

-            condition = "input.method == 'zscore' || input.method == 'plage'"

-          ),

-          radioButtons("ssgseaNorm", "ssgsea.norm:",

-                       c("True" = TRUE,

-                         "False" = FALSE)),

-          radioButtons("verbose", "verbose:",

-                       c("True" = TRUE,

-                         "False" = FALSE))

-        )))

-    )

-  )

-}

+  # CREATE REACTIVE FOR CONSOLE TEXT PROGRESS BAR

+  rout <- tempfile("consoleText", fileext = ".txt")

+  file.create(rout)

+  console.text <- reactiveFileReader(200, session, rout, readLines, warn=F)

+  

+  # ERRORS MESSAGES

+  output$errorsGsva <- renderText({

+    req(argInp$varMinsz(), argInp$varMaxsz(), argInp$selectedTau())

+    rv$errors.gsva

+  })

-gsva_validation <- function(input, output, session) {

-  success <- FALSE #Variable to control if the GSVA variables are assigned correctly

-  if(input$matrixSourceType == "fileMatrix")

-  {

-    if (is.null(input$matrixFile))

-    {

-      paste("No matrix file selected!")

-      success <- FALSE

-    }

-    else

-    {

-      #Matrix file selected

-      if(input$genesetSourceType == "fileGeneset")

-      {

-        if (is.null(input$genesetFile))

-        {

-          paste("No geneSet file selected!")

-          success <- FALSE

-        }

-        else

-        {

-          #User selects matrix file and geneSet file

-          inFile <- input$matrixFile

-          newY <- as.matrix(read.csv(inFile$datapath, header = TRUE, sep = ",")) #Reading file as matrix

-          rownames(newY) <- newY[,1] #Taking the first column as rownames

-          newY <- newY[,-1] #Deleting the first column

-          inGenesetFile <- input$genesetFile

-          genes <- getGmt(inGenesetFile$datapath)

-          if(input$maxSz == 0) {

-            varMaxsz <- Inf

-          }else {

-            varMaxsz <- input$maxSz

-          }

-          success <- TRUE

-        }

-      }

-      else

-      {

-        #User selects matrix file and geneset var

-        inFile <- input$matrixFile

-        newY <- as.matrix(read.csv(inFile$datapath, header = TRUE, sep = ",")) #Reading file as matrix

-        rownames(newY) <- newY[,1] #Taking the first column as rownames

-        newY <- newY[,-1] #Deleting the first column

-        assign("genes",get(input$genesetVar))

-        if(input$maxSz == 0) {

-          varMaxsz <- Inf

-        }else {

-          varMaxsz <- input$maxSz

-        }

-        success <- TRUE

-      }

+  # ENABLING 'RUN' BTN

+  observe({

+    if(!is.null(matrix()) && !is.null(genesets())){

+      enable("button")

+    } else {

+      disable("button")

     }

-  }

-  else

-  {

-    #User selects matrix var and geneset file

-    if(input$genesetSourceType == "fileGeneset")

-    {

-      if (is.null(input$genesetFile))

-      {

-        paste("No geneSet file selected!")

-        success <- FALSE

-      }

-      else

-      {

-        assign("newY",get(input$matrixVar))

-        inGenesetFile <- input$genesetFile

-        genes <- getGmt(inGenesetFile$datapath)

-        if(input$maxSz == 0) {

-          varMaxsz <- Inf

-        }else {

-          varMaxsz <- input$maxSz

-        }

-        success <- TRUE

-      }

-    }

-    else

-    {

-      #User selects matrix var selected and geneset var

-      assign("newY",get(input$matrixVar))

-      assign("genes",get(input$genesetVar))

-      if(input$maxSz == 0) {

-        varMaxsz <- Inf

-      }else {

-        varMaxsz <- input$maxSz

-      }

-      success <- TRUE

-    }

-  }

-  if(success==TRUE)

-  {

-    gsva_generation(input, output, session, newY, genes,varMaxsz)

-    gsva_information(input,output,session, newY, genes)

-  }

-}

+  })

+  

+  ### INPUTS ###

+  

+  # DATA MATRIX

+  matrix <- matrixServer("matrix1")

+  

+  # GENES

+  genesets <- geneSetsServer("genes1")

+  

+  # ARGUMENTS

+  argInp <- argumentsDataServer("argumentsInput")

-gsva_generation <- function(input, output, session, newY, genes,varMaxsz) {

-  x <- input$method

-  selectedTau <- NULL

-  switch (x,

-          "gsva" = {

-            selectedTau <- input$tau1

-          },

-          "ssgsea" = {

-            selectedTau <- input$tau2

-          },

-          "zscore" = {

-            selectedTau <- NULL

-          },

-          "plage" = {

-            selectedTau <- NULL

-          }

-  )

-  # GSVA Generation

-  withProgress(message = 'Runing GSVA', value = 0, {

-    incProgress(1, detail = "This may take a while...")

-    generated_gsva <<- gsva(newY, genes, method=input$method, kcdf=input$kcdf,

-                            abs.ranking=as.logical(input$absRanking),

-                            min.sz=input$minSz, max.sz=varMaxsz,

-                            parallel.sz=1L, ## by now, disable parallelism

-                            mx.diff=as.logical(input$mxDiff),

-                            tau=selectedTau,

-                            ssgsea.norm=as.logical(input$ssgseaNorm),

-                            verbose=as.logical(input$verbose))

+  #### GSVA RESULTS ####

+  

+  rv <- reactiveValues(gs=NULL, dat.t=NULL, n=NULL, dd.col=NULL, p=NULL, 

+                       errors.gsva = NULL, matrix=NULL, genesets=NULL)

+  gsva.cancel <- reactiveVal(FALSE)

+  

+  observeEvent( input$button, {

+    rv$gs <- NULL

+    rv$dat.t <- NULL

+    rv$p <- NULL

+    rv$errors.gsva = NULL

+    rv$matrix <- isolate(matrix())

+    rv$genesets <- isolate(genesets())

+    gsva.cancel(FALSE)

+    modalGSVAUI("modal.text")

+    # future() cannot take reactive values, so we must isolate() them

+    future({

+      sink(rout)

+      result <- gsva(isolate(matrix()),

+                     isolate(genesets()), 

+                     method=isolate(argInp$method()),

+                     kcdf=isolate(argInp$kcdf()),

+                     abs.ranking=isolate(argInp$absRanking()),

+                     min.sz= isolate(argInp$varMinsz()),

+                     max.sz=isolate(argInp$varMaxsz()),