deleted file mode 100644

@@ -1,3 +0,0 @@

-igsva <- function() {

-  runApp("GSVA/R/app")

-}

@@ -1,13 +1,3 @@

-#'

-#' @importFrom shiny HTML actionButton animationOptions checkboxGroupInput column div downloadHandler downloadLink eventReactive fileInput fluidPage fluidRow h2 h3 h4 headerPanel htmlOutput mainPanel need numericInput NS observe observeEvent p plotOutput reactiveValues renderPlot renderUI selectInput shinyApp sliderInput stopApp tabPanel tabsetPanel textOutput uiOutput updateSelectInput validate wellPanel withProgress conditionalPanel reactive outputOptions tableOutput tags radioButtons downloadButton

-#' @importFrom shinythemes shinytheme

-#' @importFrom utils head

-#' @importFrom geneplotter multidensity

-#' @importFrom stats median

-#' @importFrom graphics plot

-#' @export

-#'

-

 igsva <- function() {

   runApp("GSVA/R/app")

-}

\ No newline at end of file

+}

@@ -8,353 +8,6 @@

 #' @export

 #'

-selectDataInput <- function(id) {

-  # Create a namespace function using the provided id

-  ns <- NS(id)

-  

-  #UI declaration

-  column(

-    3,

-    h3("Select data source:"),

-    #Select data source

-    wellPanel(fluidRow(

-      column(

-        12,

-        #Select matrix

-        radioButtons("matrixSourceType", "Select matrix:",

-                     c("From file" = "fileMatrix",

-                       "From workspace" = "varMatrix"))

-        ,

-        #If the selected data source is a file

-        conditionalPanel(

-          condition = "input.matrixSourceType == 'fileMatrix'",

-          fileInput("matrixFile", "Choose matrix file:",

-                    accept = c(

-                      "text/csv",

-                      "text/comma-separated-values,text/plain",

-                      ".csv",".ods",".xls",".xlt")

-          )

-        ),

-        #If the selected data source is a workspace object

-        conditionalPanel(

-          condition = "input.matrixSourceType == 'varMatrix'",

-          selectInput("matrixVar", "Choose matrix var:",

-                      ls(envir=.GlobalEnv))

-        ),

-        fluidRow(column(12,

-                        HTML("<br>"))),

-        #Select geneset

-        radioButtons("genesetSourceType", "Select GeneSet:",

-                     c("From file" = "fileGeneset",

-                       "From workspace" = "varGeneset"))

-        ,

-        #If the selected data source is a file

-        conditionalPanel(

-          condition = "input.genesetSourceType == 'fileGeneset'",

-          fileInput("genesetFile", "Choose GeneSet file:",

-                    accept = ".gmt")

-        ),

-        #If the selected data source is a workspace object

-        conditionalPanel(

-          condition = "input.genesetSourceType == 'varGeneset'",

-          selectInput("genesetVar", "Choose GeneSet var:",

-                      ls(envir=.GlobalEnv))

-        ),

-        HTML("<br>"),

-        radioButtons("arg", "Control arguments:",

-                     c("No" = "no",

-                       "Yes" = "yes"))

-      )

-    ),

-    actionButton("button", "Run"))

-  )

-}

-

-mainDataInput <- function(id) {

-  # Create a namespace function using the provided id

-  ns <- NS(id)

-  

-  #UI Definition

-  mainPanel(width = 6,

-            h2("Generated GSVA data:"),

-            textOutput("information"),

-            plotOutput("plot"),

-            tableOutput("result"),

-            uiOutput("download"))

-}

-

-argumentsDataInput <- function(id) {

-  # Create a namespace function using the provided id

-  ns <- NS(id)

-  

-  #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))

-        )))

-    )

-  )

-}

-

-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

-      }

-    }

-  }

-  else

-  {

-    #User selects matrix varand 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)

-  }

-}

-

-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$minSz, max.sz=varMaxsz, parallel.sz=input$parallelSz, parallel.type=input$parallelType,

-                            mx.diff=as.logical(input$mxDiff), tau=selectedTau, ssgsea.norm=as.logical(input$ssgseaNorm),

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

-  })

-}

-

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

-  if(class(generated_gsva) == "matrix")

-  {

-    resultInformation <- matrix(data = c(input$matrixVar,input$genesetVar,ncol(generated_gsva),nrow(generated_gsva)), nrow = 1, ncol = 4)

-    colnames(resultInformation) <- c("Matrix used","GeneSet used", "Col num", "Row num")

-    output$result <- renderTable(resultInformation)

-    output$plot <- renderPlot(multidensity(as.list(as.data.frame(generated_gsva)), legend=NA, las=1, xlab=sprintf("%s scores", input$method), main="", lwd=2))

-    tagList(

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

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

-    )

-  }

-  else

-  {

-

-    resultInformation <- matrix(data = c(input$matrixVar,input$genesetVar,ncol(generated_gsva),nrow(generated_gsva)), nrow = 1, ncol = 4)

-    colnames(resultInformation) <- c("Matrix used","GeneSet used", "Col num", "Row num")

-    output$result <- renderTable(resultInformation)

-    if(class(generated_gsva) == "ExpressionSet") #If the generated gsva is an ExpressionSet

-    {

-      expressionSetObs <- exprs(generated_gsva)

-      output$plot <- renderPlot(multidensity(as.list(as.data.frame(expressionSetObs)), legend=NA, las=1, xlab=sprintf("%s scores", input$method), main="", lwd=2)) 

-    }

-    else

-    {

-      output$plot <- renderPlot(multidensity(as.list(as.data.frame(generated_gsva)), legend=NA, las=1, xlab=sprintf("%s scores", input$method), main="", lwd=2))

-    }

-    tagList(

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

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

-    )

-  }

-}

-

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

-  #Controls the Download button

-  output$downloadData <- downloadHandler(

-    filename = function() {

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

-    },

-    content = function(file) {

-      if(class(generated_gsva) == "matrix") #If the whole object is a matrix

-      {

-        dataFrameObs <- as.data.frame(generated_gsva)

-        write.csv(dataFrameObs, file)

-      }

-      else

-      {

-        if(class(generated_gsva) == "ExpressionSet") #If the generated gsva result value is an ExpressionSet

-        {

-          expressionSetObs <- exprs(generated_gsva)

-          dataFrameObs <- as.data.frame(expressionSetObs)

-          write.csv(dataFrameObs, file)

-        }

-        else

-        {

-          dataFrameObs <- as.data.frame(generated_gsva)

-          write.csv(dataFrameObs, file)

-        } 

-      }

-    }

-  )

-}

-

 igsva <- function() {

-  app <- list(ui = NULL, server = NULL)

-  app$ui <- fluidPage(theme = shinytheme("simplex"),

-                      fluidRow(

-                        selectDataInput("dataInput"),

-                        mainDataInput("mainInput")

-                        ,

-                        fluidRow(

-                          argumentsDataInput("argumentsInput")

-                        )

-                      )

-  )

-  

-  app$server <- function(input, output, session) {

-    v <- reactiveValues(action = FALSE)

-    

-    observeEvent(input$button, {

-      v$action <- input$button

-    })

-    

-    output$download <- renderUI({

-      if(v$action)

-      {

-        #Isolates the Run event, that allows the program to run the generation only if the user clicks the button.

-        isolate({

-          gsva_validation(input,output,session)

-        })

-      }

-    })

-    download_handler(input,output,session)

-    

-    #Observe the Save & Close button

-    observeEvent(input$closeSave, {

-      stopApp(generated_gsva) #Stops the app and returns the generated_gsva object

-    })

-  }

-  runApp(app)

-}

+  runApp("GSVA/R/app")

+}

\ No newline at end of file

@@ -271,17 +271,17 @@ gsva_information <- function(input, output, session) {

   else

   {

-    resultInformation <- matrix(data = c(input$matrixVar,input$genesetVar,ncol(generated_gsva$es.obs),nrow(generated_gsva$es.obs)), nrow = 1, ncol = 4)

+    resultInformation <- matrix(data = c(input$matrixVar,input$genesetVar,ncol(generated_gsva),nrow(generated_gsva)), nrow = 1, ncol = 4)

     colnames(resultInformation) <- c("Matrix used","GeneSet used", "Col num", "Row num")

     output$result <- renderTable(resultInformation)

-    if(class(generated_gsva$es.obs) == "ExpressionSet") #If the generated gsva is an ExpressionSet

+    if(class(generated_gsva) == "ExpressionSet") #If the generated gsva is an ExpressionSet

     {

-      expressionSetObs <- exprs(generated_gsva$es.obs)

+      expressionSetObs <- exprs(generated_gsva)

       output$plot <- renderPlot(multidensity(as.list(as.data.frame(expressionSetObs)), legend=NA, las=1, xlab=sprintf("%s scores", input$method), main="", lwd=2)) 

     }

     else

     {

-      output$plot <- renderPlot(multidensity(as.list(as.data.frame(generated_gsva$es.obs)), legend=NA, las=1, xlab=sprintf("%s scores", input$method), main="", lwd=2))

+      output$plot <- renderPlot(multidensity(as.list(as.data.frame(generated_gsva)), legend=NA, las=1, xlab=sprintf("%s scores", input$method), main="", lwd=2))

     }

     tagList(

       downloadButton('downloadData', 'Download'),

@@ -304,15 +304,15 @@ download_handler <- function(input, output, session) {

       }

       else

       {

-        if(class(generated_gsva$es.obs) == "ExpressionSet") #If the generated gsva es.obs is an ExpressionSet

+        if(class(generated_gsva) == "ExpressionSet") #If the generated gsva result value is an ExpressionSet

         {

-          expressionSetObs <- exprs(generated_gsva$es.obs)

+          expressionSetObs <- exprs(generated_gsva)

           dataFrameObs <- as.data.frame(expressionSetObs)

           write.csv(dataFrameObs, file)

         }

         else

         {

-          dataFrameObs <- as.data.frame(generated_gsva$es.obs)

+          dataFrameObs <- as.data.frame(generated_gsva)

           write.csv(dataFrameObs, file)

         } 

       }

@@ -98,16 +98,13 @@ argumentsDataInput <- function(id) {

           12,

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

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

-          radioButtons("rnaseq", "Rnaseq:",

-                       c("False" = FALSE,

-                         "True" = TRUE)),

+          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("noBootstraps","no.bootstraps:",value = 0),

-          numericInput("bootstrapPercent","bootstrap.percent:",value = .632),

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

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

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

@@ -125,9 +122,6 @@ argumentsDataInput <- function(id) {

           conditionalPanel(

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

           ),

-          radioButtons("kernel", "kernel:",

-                       c("True" = TRUE,

-                         "False" = FALSE)),

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

                        c("True" = TRUE,

                          "False" = FALSE)),

@@ -255,10 +249,10 @@ gsva_generation <- function(input, output, session, newY, genes,varMaxsz) {

   #GSVA Generation

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

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

-    generated_gsva <<- gsva(newY, genes, method = input$method, rnaseq = as.logical(input$rnaseq), abs.ranking = as.logical(input$absRanking),

-                            min.sz = input$minSz, max.sz = varMaxsz, no.bootstraps = input$noBootstraps, bootstrap.percent = input$bootstrapPercent, 

-                            parallel.sz = input$parallelSz, parallel.type = input$parallelType, mx.diff = as.logical(input$mxDiff), tau = selectedTau, kernel = as.logical(input$kernel),

-                            ssgsea.norm = as.logical(input$ssgseaNorm), verbose = as.logical(input$verbose)) #Result asignation

+    generated_gsva <<- gsva(newY, genes, method=input$method, kcdf=input$kcdf, abs.ranking=as.logical(input$absRanking),

+                            min.sz=input$minSz, max.sz=varMaxsz, parallel.sz=input$parallelSz, parallel.type=input$parallelType,

+                            mx.diff=as.logical(input$mxDiff), tau=selectedTau, ssgsea.norm=as.logical(input$ssgseaNorm),

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

   })

 }

new file mode 100644

@@ -0,0 +1,366 @@

+#'

+#' @importFrom shiny HTML actionButton animationOptions checkboxGroupInput column div downloadHandler downloadLink eventReactive fileInput fluidPage fluidRow h2 h3 h4 headerPanel htmlOutput mainPanel need numericInput NS observe observeEvent p plotOutput reactiveValues renderPlot renderUI selectInput shinyApp sliderInput stopApp tabPanel tabsetPanel textOutput uiOutput updateSelectInput validate wellPanel withProgress conditionalPanel reactive outputOptions tableOutput tags radioButtons downloadButton

+#' @importFrom shinythemes shinytheme

+#' @importFrom utils head

+#' @importFrom geneplotter multidensity

+#' @importFrom stats median

+#' @importFrom graphics plot

+#' @export

+#'

+

+selectDataInput <- function(id) {

+  # Create a namespace function using the provided id

+  ns <- NS(id)

+  

+  #UI declaration

+  column(

+    3,

+    h3("Select data source:"),

+    #Select data source

+    wellPanel(fluidRow(

+      column(

+        12,

+        #Select matrix

+        radioButtons("matrixSourceType", "Select matrix:",

+                     c("From file" = "fileMatrix",

+                       "From workspace" = "varMatrix"))

+        ,

+        #If the selected data source is a file

+        conditionalPanel(

+          condition = "input.matrixSourceType == 'fileMatrix'",

+          fileInput("matrixFile", "Choose matrix file:",

+                    accept = c(

+                      "text/csv",

+                      "text/comma-separated-values,text/plain",

+                      ".csv",".ods",".xls",".xlt")

+          )

+        ),

+        #If the selected data source is a workspace object

+        conditionalPanel(

+          condition = "input.matrixSourceType == 'varMatrix'",

+          selectInput("matrixVar", "Choose matrix var:",

+                      ls(envir=.GlobalEnv))

+        ),

+        fluidRow(column(12,

+                        HTML("<br>"))),

+        #Select geneset

+        radioButtons("genesetSourceType", "Select GeneSet:",

+                     c("From file" = "fileGeneset",

+                       "From workspace" = "varGeneset"))

+        ,

+        #If the selected data source is a file

+        conditionalPanel(

+          condition = "input.genesetSourceType == 'fileGeneset'",

+          fileInput("genesetFile", "Choose GeneSet file:",

+                    accept = ".gmt")

+        ),

+        #If the selected data source is a workspace object

+        conditionalPanel(

+          condition = "input.genesetSourceType == 'varGeneset'",

+          selectInput("genesetVar", "Choose GeneSet var:",

+                      ls(envir=.GlobalEnv))

+        ),

+        HTML("<br>"),

+        radioButtons("arg", "Control arguments:",

+                     c("No" = "no",

+                       "Yes" = "yes"))

+      )

+    ),

+    actionButton("button", "Run"))

+  )

+}

+

+mainDataInput <- function(id) {

+  # Create a namespace function using the provided id

+  ns <- NS(id)

+  

+  #UI Definition

+  mainPanel(width = 6,

+            h2("Generated GSVA data:"),

+            textOutput("information"),

+            plotOutput("plot"),

+            tableOutput("result"),

+            uiOutput("download"))

+}

+

+argumentsDataInput <- function(id) {

+  # Create a namespace function using the provided id

+  ns <- NS(id)

+  

+  #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")),

+          radioButtons("rnaseq", "Rnaseq:",

+                       c("False" = FALSE,

+                         "True" = TRUE)),

+          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("noBootstraps","no.bootstraps:",value = 0),

+          numericInput("bootstrapPercent","bootstrap.percent:",value = .632),

+          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("kernel", "kernel:",

+                       c("True" = TRUE,

+                         "False" = FALSE)),

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

+                       c("True" = TRUE,

+                         "False" = FALSE)),

+          radioButtons("verbose", "verbose:",

+                       c("True" = TRUE,

+                         "False" = FALSE))

+        )))

+    )

+  )

+}

+

+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

+      }

+    }

+  }

+  else

+  {

+    #User selects matrix varand 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)

+  }

+}

+

+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$method, rnaseq = as.logical(input$rnaseq), abs.ranking = as.logical(input$absRanking),

+                            min.sz = input$minSz, max.sz = varMaxsz, no.bootstraps = input$noBootstraps, bootstrap.percent = input$bootstrapPercent, 

+                            parallel.sz = input$parallelSz, parallel.type = input$parallelType, mx.diff = as.logical(input$mxDiff), tau = selectedTau, kernel = as.logical(input$kernel),

+                            ssgsea.norm = as.logical(input$ssgseaNorm), verbose = as.logical(input$verbose)) #Result asignation

+  })

+}

+

+gsva_information <- function(input, output, session) {

+  if(class(generated_gsva) == "matrix")

+  {

+    resultInformation <- matrix(data = c(input$matrixVar,input$genesetVar,ncol(generated_gsva),nrow(generated_gsva)), nrow = 1, ncol = 4)

+    colnames(resultInformation) <- c("Matrix used","GeneSet used", "Col num", "Row num")

+    output$result <- renderTable(resultInformation)

+    output$plot <- renderPlot(multidensity(as.list(as.data.frame(generated_gsva)), legend=NA, las=1, xlab=sprintf("%s scores", input$method), main="", lwd=2))

+    tagList(

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

+      actionButton('closeSave','Save & Close')

+    )

+  }

+  else

+  {

+

+    resultInformation <- matrix(data = c(input$matrixVar,input$genesetVar,ncol(generated_gsva$es.obs),nrow(generated_gsva$es.obs)), nrow = 1, ncol = 4)

+    colnames(resultInformation) <- c("Matrix used","GeneSet used", "Col num", "Row num")

+    output$result <- renderTable(resultInformation)

+    if(class(generated_gsva$es.obs) == "ExpressionSet") #If the generated gsva is an ExpressionSet

+    {

+      expressionSetObs <- exprs(generated_gsva$es.obs)

+      output$plot <- renderPlot(multidensity(as.list(as.data.frame(expressionSetObs)), legend=NA, las=1, xlab=sprintf("%s scores", input$method), main="", lwd=2)) 

+    }

+    else

+    {

+      output$plot <- renderPlot(multidensity(as.list(as.data.frame(generated_gsva$es.obs)), legend=NA, las=1, xlab=sprintf("%s scores", input$method), main="", lwd=2))

+    }

+    tagList(

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

+      actionButton('closeSave','Save & Close')

+    )

+  }

+}

+

+download_handler <- function(input, output, session) {

+  #Controls the Download button

+  output$downloadData <- downloadHandler(

+    filename = function() {

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

+    },

+    content = function(file) {

+      if(class(generated_gsva) == "matrix") #If the whole object is a matrix

+      {

+        dataFrameObs <- as.data.frame(generated_gsva)

+        write.csv(dataFrameObs, file)

+      }

+      else

+      {

+        if(class(generated_gsva$es.obs) == "ExpressionSet") #If the generated gsva es.obs is an ExpressionSet

+        {

+          expressionSetObs <- exprs(generated_gsva$es.obs)

+          dataFrameObs <- as.data.frame(expressionSetObs)

+          write.csv(dataFrameObs, file)

+        }

+        else

+        {

+          dataFrameObs <- as.data.frame(generated_gsva$es.obs)

+          write.csv(dataFrameObs, file)

+        } 

+      }

+    }

+  )

+}

+

+igsva <- function() {

+  app <- list(ui = NULL, server = NULL)

+  app$ui <- fluidPage(theme = shinytheme("simplex"),

+                      fluidRow(

+                        selectDataInput("dataInput"),

+                        mainDataInput("mainInput")

+                        ,

+                        fluidRow(

+                          argumentsDataInput("argumentsInput")

+                        )

+                      )

+  )

+  

+  app$server <- function(input, output, session) {

+    v <- reactiveValues(action = FALSE)

+    

+    observeEvent(input$button, {

+      v$action <- input$button

+    })

+    

+    output$download <- renderUI({

+      if(v$action)

+      {

+        #Isolates the Run event, that allows the program to run the generation only if the user clicks the button.

+        isolate({

+          gsva_validation(input,output,session)

+        })

+      }

+    })

+    download_handler(input,output,session)

+    

+    #Observe the Save & Close button

+    observeEvent(input$closeSave, {

+      stopApp(generated_gsva) #Stops the app and returns the generated_gsva object

+    })

+  }

+  runApp(app)

+}