Activate export button

LoadPackages.R

@@ -51,13 +51,13 @@ if (!require(circlize)) {
 if(!require(BiocManager)){
   install.packages("BiocManager")
 }
-if (!require(genefilter)) {
-  BiocManager::install("genefilter", ask=FALSE)
-}
-
-if(!require("SummarizedExperiment")){
-  BiocManager::install("SummarizedExperiment", ask=FALSE)
-}
+# if (!require(genefilter)) {
+#   BiocManager::install("genefilter", ask=FALSE)
+# }
+# 
+# if(!require("SummarizedExperiment")){
+#   BiocManager::install("SummarizedExperiment", ask=FALSE)
+# }
 
 if (!require(googleVis)) {
   install.packages('googleVis',  repos="https://cran.univ-paris1.fr/")

server.R

@@ -14,6 +14,7 @@ shinyServer(function(input, output,session) {
   file.create(namesfile,showWarnings=FALSE)
   target = NULL
   taxo = NULL
+  proxy = dataTableProxy('DataTaxo')
   
   ## JSON name for masque
   curdir  = getwd()
@@ -264,6 +265,7 @@ shinyServer(function(input, output,session) {
     Counts = NULL
     inputData = NULL
     target = NULL
+    
     if(input$FileFormat=="fileCounts")
     {
       Counts = dataInputCounts()
@@ -319,7 +321,6 @@ shinyServer(function(input, output,session) {
     #         percent = inputData$percent
     #       }
     #     }
-    
     return(list(data=data,check=check,percent=percent))
   })
   
@@ -364,11 +365,6 @@ shinyServer(function(input, output,session) {
     return(list(Check = Check,Error = Error,normFactors=normFactors))
   })
   
-  
-  
-  
-  
-  
   ## Merge counts data
   dataMergeCounts <-reactive({
     input$RunDESeq
@@ -626,11 +622,7 @@ shinyServer(function(input, output,session) {
     options = list(lengthMenu = list(c(10, 50, -1), c('10', '50', 'All')),
                                      pageLength = 10,scrollX=TRUE, processing=FALSE)
 )
-  # "table.on('click', '#DataTaxo button', function () {
-  #                    Shiny.onInputChange('lastClickId',this.id);
-  #                    Shiny.onInputChange('lastClick', Math.random())
-  #                  );")
-  proxy = dataTableProxy('DataTaxo')
+
   observeEvent(input$DataTaxo_cell_edit, {
     info = input$DataTaxo_cell_edit
     str(info)
@@ -652,7 +644,7 @@ shinyServer(function(input, output,session) {
       res = tabBox(width = NULL, selected = "Count table",
                    tabPanel("Count table",DT::dataTableOutput("DataCounts")),
                    tabPanel("Taxonomy",DT::dataTableOutput("DataTaxo"), 
-                            actionButton("deleteTax", "Delete annotation"),
+                            actionButton("deleteTaxo", "Delete annotation"),
                             downloadButton('ExportTaxo', 'Export taxonomy file')),
                    tabPanel("Summary",h5(strong("Percentage of annotation")),htmlOutput("SummaryView"),
                             br(),h5(strong("Number of features by level:")),plotOutput("SummaryViewBarplot",width = 1200,height=500)),
@@ -665,7 +657,7 @@ shinyServer(function(input, output,session) {
       res = tabBox(width = NULL,selected = "Count table",
                    tabPanel("Count table",DT::dataTableOutput("DataCounts")),
                    tabPanel("Taxonomy",DT::dataTableOutput("DataTaxo"),
-                            actionButton("deleteTax", "Delete annotation"),
+                            actionButton("deleteTaxo", "Delete annotation"),
                             downloadButton('ExportTaxo', 'Export taxonomy file')),
                    tabPanel("Summary",h5(strong("Percentage of annotation")),htmlOutput("SummaryView"),
                             br(),h5(strong("Number of features by level:")),plotOutput("SummaryViewBarplot",width = 1200,height=500))
@@ -2005,7 +1997,7 @@ shinyServer(function(input, output,session) {
   ######################## END MASQUE #################################
   
   
-  observeEvent(input$deleteTax,{
+  observeEvent(input$deleteTaxo,{
     if(is.null(values$TaxoWorking)) values$TaxoWorking= dataInput()$data$taxo
     if (!is.null(input$DataTaxo_rows_selected)) {
       
@@ -2077,6 +2069,25 @@ shinyServer(function(input, output,session) {
     return(res)
   })
   
+  # ## Vis button
+  # output$VisButton <- renderUI({
+  #   
+  #   res = NULL
+  #   ChTM = "Error"
+  #   target = values$TargetWorking
+  #   labeled = values$labeled
+  #   CT = dataInput()$data$counts
+  #   taxo = input$TaxoSelect
+  #   VarInt = input$InterestVar
+  #   
+  #   ## Return NULL if there is no error
+  #   if(!is.null(CT) && length(VarInt)>=1) ChTM = CheckTargetModel(input,target,labeled,CT)$Error
+  #   
+  #   if(!is.null(target) && taxo!="..." && is.null(ChTM) && length(VarInt)>=1) res = actionButton("RunDESeq",strong("Run analysis"),icon = icon("caret-right"))
+  #   
+  #   return(res)
+  # })
+  
   ## Var for normalization
   output$SelectVarNorm <- renderUI({
     
@@ -2196,6 +2207,10 @@ shinyServer(function(input, output,session) {
                            observation_metadata=dataInput()$data$taxo_biom), file)}
   )
   
+  output$ExportTaxo <- downloadHandler(
+    filename = function() { 'SHAMAN_taxo.csv' },
+    content = function(file){write.csv(dataInput()$data$taxo, file)}
+  )
   ## Export in .csv
   output$ExportCounts <- downloadHandler(
     filename = function() { 'NormCounts.csv' },

ui.R

@@ -632,6 +632,7 @@ function(request) {
                              fluidRow( 
                                column(width=6,uiOutput('ButtonBiom')),
                                #column(width=6,downloadButton('ExportBiom', 'Export BIOM')),
+                               #uiOutput("VisButton"),
                                column(width=6,uiOutput("RunButton"))
                              )
                          ),