add getdegenes to MATRiX

function/decideTestTrix.R

@@ -23,16 +23,15 @@
 #'
 #' @export
 
-decTestTRiX <- function(adj,logfc,pval, DEGcutoff = 0.05 ,FC = 1,cutoff_meth = "FDR",maxDE = NULL,contrast = 1:ncol(adj))
-
-{
+decTestTRiX <- function(adj,logfc,pval, DEGcutoff = 0.05 ,FC = 1,cutoff_meth = "FDR",maxDE = NULL,contrast = 1:ncol(adj)){
   ## select probes with cutoff_meth<= DEGcutoff and FoldChange > FC and nbr of selected probes < maxDE (if nb FC selected >maxDE)
 
 
   if (length(contrast) == 1)
     contrast = c(contrast, contrast)
 
 
+
   if (is.na(maxDE) || is.null(maxDE))
     maxDE = nrow(adj)
 
@@ -41,18 +40,19 @@ decTestTRiX <- function(adj,logfc,pval, DEGcutoff = 0.05 ,FC = 1,cutoff_meth = "
     pList = adj[, contrast]
 
 
+
   if(cutoff_meth=="None")
     pList= pval[,contrast]
 
 
   ## select on pvalue
   DEp = pList <= DEGcutoff
+
 
 
   ## select on FC
   DEFC = 2 ** abs(logfc[, contrast]) >= FC
 
-
   ## reduce selection to maxDE
   if (any(colSums(DEFC) > maxDE)) {
 
@@ -84,7 +84,6 @@ decTestTRiX <- function(adj,logfc,pval, DEGcutoff = 0.05 ,FC = 1,cutoff_meth = "
   DEsel = which(rowSums(DEsel, na.rm = T) > 0)
   elements= list(DEsel, length(DEsel))
 
-
   return(elements)
 
 }

function/vennplot.R

@@ -204,7 +204,6 @@ Vennfinal <- function(myl,adj, cex=1, cutoffpval, cutofffc, statimet, meandup =
 #'
 
 myventocsv <- function(myven, adj){
-
   max.length <- max(sapply(myven, length))
   myven %>% lapply(function(v){ c(v, rep("", max.length-length(v)))}) %>% setNames(names(adj)) %>% as.data.frame()
 }
@@ -221,7 +220,6 @@ myventocsv <- function(myven, adj){
 
 
 mysetventocsv <- function(myven){
-
   max.length <- max(sapply(myven, length))
   myven %>%lapply(function(v){ c(v, rep("", max.length-length(v)))}) %>% as.data.frame()
 }

global.R

@@ -54,8 +54,8 @@ source("./module/Selgroup.R")
 source("./module/enrichmodule.R")
 source("./module/groupcol.R")
 source("./module/magnificentables.R")
-source("./module/tablexport.R")
-
+source("./module/Savemoduletable.R")
+source("./module/getdegenes.R")
 
 
 ################################

module/Savemoduletable.R

@@ -0,0 +1,85 @@
+#' downloadFilestab is a shiny widget which aims is to download a reactive plot
+#'
+#' @param id Shiny id
+#' @param label Shiny label
+#'
+#' @return Widget in the gui
+#'
+#' @export
+#'
+
+downloadFilestab <- function(id, label = "Save your Scree plot") {
+  ns <- NS(id)
+  downloadButton(ns("downloadtable"), label ,   style ="color: #fff; background-color: #337ab7; border-color: #2e6da4")
+}
+
+
+
+#' downoutputables is a shiny module which aims is to export reactive table
+#'
+#' @param input Internal
+#' @param output Internal
+#' @param session Internal
+#' @param projectname A reactive character (MA project or session data)
+#' @param suffix A character
+#' @param data A reactive expression to be plot
+#' @param cont A reactive character vector of the selected comparison(s)
+#' @param case A numeric value
+#' @param xlsx A boolean value
+#'
+#' @export
+#'
+
+downoutputables <- function(input, output, session , projectname, suffix = "plot.csv",  data = NULL , cont = NULL,  xlsx = F , case ) {
+
+
+
+  output$downloadtable  <- downloadHandler(
+
+    filename <- function() {
+
+      paste0(basename(file_path_sans_ext(projectname())), suffix  , sep ='')},
+
+
+    content <- function(file) {
+
+    if(!xlsx)  
+      write.table(try(switch(case, 
+                   myventocsv(data()  ,cont()), 
+                   mysetventocsv(setvglobalvenn(data(), cont(), dll =T )),
+                   data())),
+        file,
+        na = "",
+        row.names = F,
+        col.names = T,
+        append = TRUE,
+        sep = ";"
+      )
+    else
+      withProgress(message = 'Creation of the xlsx table:',
+                   value = 0, {
+                     n <- NROW(50)
+                     for (i in 1:n) {
+                       incProgress(1 / n, detail = "Please wait...")
+                     }
+
+
+                     library(xlsx)
+
+                     for (i in 1:length(data())) {
+                       if (i == 1)
+                         write.xlsx(file = file,data()[[i]],
+                                    sheetName = paste("Cluster", i))
+                       else
+                         write.xlsx(
+                           file = file,
+                           data()[[i]],
+                           sheetName = paste("Cluster", i),
+                           append = TRUE
+                         )
+                     }
+                   })
+
+    })
+
+}

module/Selgroup.R

@@ -38,42 +38,50 @@ checkboxElements <- function(id){
 #'
 
 boxChooser <- function(input, output, session, label, data, group, case, empty =F) {
+
+  isinline <- reactiveValues(inline = F)
+
+  observe({
+    req(group()[[2]]$Grp)
+    isinline$format <- ifelse(length(levels(group()[[2]]$Grp)) >= 6, T, F)
+  })
 
   output$usercheck <- renderUI({
-
+    
     ns <- session$ns
+    groupinline <- ifelse(length(levels(group()[[2]]$Grp)) >= 6, T, F)
     case = ifelse(empty,  2, 1)
     checkboxGroupInput(
       ns("box"),
       label,
       choices =data(),
       selected =  switch(case,data(), NULL),
-      inline = ifelse(length(levels(group()[[2]]$Grp)) > 6, T, F)
+      inline = isinline$format
     )
 
   })
 
   #Select all the contrasts
   observeEvent(input$allcomphm, {
-    groupinline = ifelse(length(levels(group()[[2]]$Grp)) > 6, T, F)
+    #groupinline = ifelse(length(levels(group()[[2]]$Grp)) >= 6, T, F)
     updateCheckboxGroupInput(
       session,
       "box",
       label ,
       choices = data(),
       selected = data(),
-      inline = groupinline
+      inline = isinline$format
     )
   })
 
   #Unselect all the contrasts
   observeEvent(input$nocomphm, {
-    groupinline = ifelse(length(levels(group()[[2]]$Grp)) > 6, T, F)
+    #groupinline = ifelse(length(levels(group()[[2]]$Grp)) >= 6, T, F)
     updateCheckboxGroupInput(session,
                              "box",
                              label ,
                              choices = data(),
-                             inline= groupinline
+                             inline= isinline$format
     )
   })