add start to go

function/formating.R

@@ -261,7 +261,7 @@ heatmtoclust = function( hmp01_All, exprData, pval, myval= 5){
   mygen = as.integer(row.names(final))
 
   heatmclust = pval %>%
-    select (X,GeneName) %>%
+    dplyr::select (X,GeneName) %>%
     filter( X %in% mygen) %>%
     left_join(data.frame(X=mygen), . , by="X") %>%
     arrange(-row_number())

server.R

@@ -1,3 +1,7 @@
+###############################
+######## Loading functions    #
+###############################
+
 source("function/heatmtruncated.R")
 source("function/formating.R")
 source("function/PCA.R")
@@ -6,9 +10,16 @@ source("function/decideTestTrix.R")
 source("function/vennplot.R")
 source("function/create_forked_task.R")
 source("function/cutheat.R")
+
+###############################
+######## creating graph log   #
+###############################
+
+
 # options(shiny.reactlog=TRUE)
 # showReactLog(time = TRUE)
 
+
 shinyServer(server <- function(input, output, session) {
 
   ###############################

server/heatmapshiny.R

@@ -4,7 +4,6 @@
 
 
 
-
 #' rowname is a reactive function which aim is to hide or show the rownames
 #'
 #' @param input$rowname  a boolean radio button input
@@ -38,18 +37,75 @@ colname <- reactive({
 
 heatmapobj <- NULL # declare outside the observeEvent
 formatidus <- NULL
+hmbis <- reactiveValues()
+hmobj <- reactiveValues()
+
 
 observe({
 
   heatid <- input$matrixapp
   if (grepl("Heatmap", heatid)) {
-    formatidus <<- length(formated())
+    formatidus <<- length(formated()) # doit trouver une autre valeur que formated pour donner la taille
     if (formatidus < 2000)
       source(file.path("server", "plotreact.R"), local = TRUE)$value #
-    else
-      source(file.path("server", "plotreact2.R"), local = TRUE)$value #
+   else
+     source(file.path("server", "plotreact2.R"), local = TRUE)$value #
   }
+
+
+
+# observe({
+#   obj <- hmobj$hm 
+#   print(obj)
+# 
+# })
+
+
+output$save <- downloadHandler(filename <- function() {
+  paste0(basename(file_path_sans_ext("myfile")),
+         '_heatmap.',
+         input$form,
+         sep = '')
+},
+content <- function(file) {
+  if (input$form == "emf")
+
+    emf(
+      file,
+      width = 7,
+      height = 7,
+      pointsize = 12,
+      coordDPI = 300
+    )
 
+  else if (input$form == "png")
+    png(
+      file,
+      width = 900,
+      height = 1200,
+      units = "px",
+      pointsize = 12,
+      res = 100
+    )
+  else
+    eps(file,
+        width = 7,
+        height = 7)
+
+  if (!is.null(formated()))
+    withProgress(message = 'Saving heatmap:',
+                 value = 0, {
+                   n <- NROW(formated())
+                   for (i in 1:n) {
+                     incProgress(1 / n, detail = "Please wait...")
+                   }
+                   heatmapfinal(isplot = F)
+                 })
+  dev.off()
+
+  })
+
+
   output$downloadcut <- downloadHandler(
     filename = function() {
       paste(basename(file_path_sans_ext(input$filename)),
@@ -62,9 +118,13 @@ observe({
     }
   )
 
-  output$clustering <- renderDataTable(heatmapfinal(isplot = T)) # Summary of the significant genes depending on the pvalue with FC set to (1.2,2,4,6,10)
+  output$clustering <-
+    renderDataTable(heatmapfinal(isplot = T)) # Summary of the significant genes depending on the pvalue with FC set to (1.2,2,4,6,10)
 })
 
+
+obsC <- observe(quote({ print(formatidus) }), quoted = TRUE)
+
 # cutedhm <- reactive({
 #   req(hm())
 #   cut02 = cut(hm()$rowDendrogram, h = input$cutheatm)

server/plotreact.R

@@ -29,10 +29,13 @@
 #' 
 
 
+shinyjs::disable("heatm")
+
 heatmapfinal <- function(isplot  = T) {
+
   plotHeatmaps(
     hmbis()[[1]],
-    formated(),
+    formated(), 
     droplevels(new_group()$Grp),
     workingPath = wd_path,
     my_palette = colorRampPalette(c(
@@ -52,6 +55,7 @@ heatmapfinal <- function(isplot  = T) {
     gpcolr = hmbis()[[6]],
     distfunTRIX = hmbis()[[2]]
   )
+
 }
 
 #' hmbis is an event reactive function that pre-computed hierarchical clustering on microarray data 
@@ -72,12 +76,11 @@ heatmapfinal <- function(isplot  = T) {
 
 
 hmbis <- reactive( {
-  #hmbis <- eventReactive(input$heatm, {
-
-  isolate( # isolate in order to avoid that reactive values update the heatmap 
+
+  #isolate( # isolate in order to avoid that reactive values update the heatmap 
     truncatedhat(
       data.matrix(new_data()),
-      formated(),
+      isolate(formated()), 
       droplevels(new_group()$Grp),
       workingPath = wd_path,
       k = input$clusters,
@@ -86,81 +89,36 @@ hmbis <- reactive( {
       Coldistfun = input$dist,
       meanGrp = input$meangrp
     )
-  )
+
+  #)
 })
 
-#heatmapobj <<- hmbis() # a static variable 
 
+hm <- reactive({
+  heatmapfinal(isplot = F)
+})
 
 
 output$distPlot <- renderPlot({
-  isolate({
+  #isolate({
     if (!is.null(formated()))
       withProgress(message = 'Plotting heatmap:', # Add sliderbar when loading heatmap
                    value = 0,
                    {
                      n <- NROW(formated()) #number of row in the formated dataframe
-
+                     if (n >2000)
+                       return(isolate(heatmapfinal(isplot = F)))
                      for (i in 1:n) {
                        incProgress(1 / n, detail = "Please wait...")
                      }
-                     hmbis()
+                     isolate(hmbis())
                      heatmapfinal(isplot = F)
-                   })
-  })
+                     #hmobj$hm <- (hm())
+
+ })
 }, width = 900 , height = 1200, res = 100)
 
 
-output$save <- downloadHandler(filename <- function() {
-  paste0(basename(file_path_sans_ext("myfile")),
-         '_heatmap.',
-         input$form,
-         sep = '')
-},
-content <- function(file) {
-  if (input$form == "emf")
-
-    emf(
-      file,
-      width = 7,
-      height = 7,
-      pointsize = 12,
-      coordDPI = 300
-    )
-
-  else if (input$form == "png")
-    png(
-      file,
-      width = 900,
-      height = 1200,
-      units = "px",
-      pointsize = 12,
-      res = 100
-    )
-  else
-    eps(file,
-        width = 7,
-        height = 7)
-
-  if (!is.null(formated()))
-    withProgress(message = 'Saving heatmap:',
-                 value = 0,
-                 {
-                   n <- NROW(formated())
-
-                   for (i in 1:n) {
-                     incProgress(1 / n, detail = "Please wait...")
-                   }
-
-                   heatmapfinal(isplot = F)
-
-                 })
-
-  dev.off()
-
-
-})
-
 
 
 

server/plotreact2.R

@@ -27,8 +27,11 @@
 #' 
 #' @export
 #' 
-
-
+
+  shinyjs::enable("heatm")
+
+
+
   heatmapfinal <- function(isplot  = T) {
     plotHeatmaps(
       heatmapobj[[1]],
@@ -55,6 +58,7 @@
   }
 
 
+
   #' hmbis is an event reactive function that pre-computed hierarchical clustering on microarray data 
   #'
   #' @param new_data a data frame with all the individuals selected
@@ -109,53 +113,4 @@
   }, width = 900 , height = 1200, res = 100)
 
 
-  output$save <- downloadHandler(filename <- function() {
-    paste0(basename(file_path_sans_ext("myfile")),
-           '_heatmap.',
-           input$form,
-           sep = '')
-  },
-  content <- function(file) {
-    if (input$form == "emf")
-
-      emf(
-        file,
-        width = 7,
-        height = 7,
-        pointsize = 12,
-        coordDPI = 300
-      )
-
-    else if (input$form == "png")
-      png(
-        file,
-        width = 900,
-        height = 1200,
-        units = "px",
-        pointsize = 12,
-        res = 100
-      )
-    else
-      eps(file,
-          width = 7,
-          height = 7)
-
-    if (!is.null(formated()))
-      withProgress(message = 'Saving heatmap:',
-                   value = 0,
-                   {
-                     n <- NROW(formated())
-
-                     for (i in 1:n) {
-                       incProgress(1 / n, detail = "Please wait...")
-                     }
-
-                     heatmapfinal(isplot = F)
-
-                   })
-
-    dev.off()
-
-
-  })
-
+