@@ -10,13 +10,13 @@ plot3_Server <- function(id, eventData2, rv, matrix, genesets){

       output$plot3 <- renderPlotly({

         req(eventData2())

         selected.gene.set <- rv$p2$x$data[[1]]$text[eventData2()]

-        if(is(genesets, "GeneSetCollection")){

-          genes.toplot <- geneIds(genesets)[[selected.gene.set]]

+        if(is(genesets(), "GeneSetCollection")){

+          genes.toplot <- geneIds(genesets())[[selected.gene.set]]

         } else {

-          genes.toplot <- genesets[[selected.gene.set]]

+          genes.toplot <- genesets()[[selected.gene.set]]

         }

-        mt <- match(genes.toplot, rownames(matrix))

-        x <-  matrix[na.omit(mt), rv$sample.c]

+        mt <- match(genes.toplot, rownames(matrix()))

+        x <-  matrix()[na.omit(mt), rv$sample.c]

         df <- as.data.frame(x)

         df$x <- as.numeric(df$x)

         df$Gene <- rownames(df)

@@ -25,7 +25,7 @@ plot3_Server <- function(id, eventData2, rv, matrix, genesets){

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

           geom_rug() + theme(legend.position = "none") +

           labs(x="Gene Expressions in selected sample", y="Density") +

-          xlim(as.numeric(range(matrix))) +

+          xlim(as.numeric(range(matrix()))) +

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

         ggplotly(rv$p3, tooltip = c("Gene", "x")) %>% style(hoverinfo="none", traces = 1) %>%

           layout(title = list(text = paste0('<br><sup><i>', selected.gene.set, '</i></sup>'),

@@ -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))