@@ -12,7 +12,7 @@ argumentsDataUI <- function(id) {

         column(

           12,

           selectInput(ns("method"), "Choose method:",

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

+                      choices = methodChoices),

           selectInput(ns("kcdf"), "Choose kcdf:",

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

           radioButtons(ns("absRanking"), "abs.ranking:",

@@ -20,4 +20,9 @@ source("plot3_Module.R")

 source("matrixModule.R")

 source("geneSetsModule.R")

 source("argumentsDataModule.R")

-source("closeModule.R")

\ No newline at end of file

+source("closeModule.R")

+

+methodChoices <- c( "GSVA" = "gsva",

+                    "ssGSEA" = "ssgsea",

+                    "zscore" = "zscore",

+                    "PLAGE" = "plage")

\ No newline at end of file

@@ -10,9 +10,14 @@ plot1_Server <- function(id, rv){

       output$plot <- renderPlotly({

         req(rv$dat.t)

+        # in order to print the name of the method (and not the 

+        # selected value from the method) on the 'x' label, this

+        # name is retrieved from the list 'methodChoices' declared

+        # in 'global.R

+        method <- names(methodChoices)[methodChoices == rv$method]

         rv$p <- ggplot(data = rv$dat.t, aes(x=value, color=Sample)) +

           stat_density(geom="line", position = "identity") +

-          theme(legend.position = "none") + labs(x="GSVA Scores", y="Density") +

+          theme(legend.position = "none") + labs(x=paste0(method, " Scores"), y="Density") +

           scale_color_manual("Legend", values = rv$dd.col)

         ggplotly(rv$p, tooltip = "Sample", source = "click1")

       })

@@ -10,11 +10,18 @@ plot2_Server <- function(id, eventData1, rv){

       output$plot2 <- renderPlotly({

         req(eventData1())

+        

+        # in order to print the name of the method (and not the 

+        # selected value from the method) on the 'x' label, this

+        # name is retrieved from the list 'methodChoices' declared

+        # in 'global.R

+        method <- names(methodChoices)[methodChoices == rv$method]

+        

         rv$sample.c <- colnames(rv$gs)[eventData1()]

         data <- rv$dat.t[Sample==rv$sample.c]

         p <- ggplot(data = data, aes(x=value, color=Sample)) +

           stat_ecdf(geom="point") + theme(legend.position = "none") +

-          labs(x="GSVA Scores in selected sample", y="Empirical Cumulative Density") +

+          labs(x=paste0(method, " Scores in selected sample"), y="Empirical Cumulative Density") +

           scale_color_manual("Legend", values = rv$dd.col)

         rv$p2 <- ggplotly(p, source="click2") %>% style(text=data$gene.sets)

         rv$p2

@@ -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