transfo switch

panels/dataInput.R

@@ -119,9 +119,9 @@ output$dataUI <- renderUI({
 })
 
 observeEvent(input$okData, {
-  physeq(NULL)
+  raw_physeq(NULL)
   try(
-    physeq(
+    raw_physeq(
       switch(
         input$dataset,
         "demo" =
@@ -171,7 +171,8 @@ observeEvent(input$okData, {
     outFile = showModal(dataInput(failed = TRUE))
     )
   
-  if (inherits(physeq(), "phyloseq")) {
+  if (inherits(raw_physeq(), "phyloseq")) {
+    physeq(raw_physeq())
     message(paste("[Easy16S] Correct upload with", input$dataset, "mode :", message))
     removeModal()
   } else {
@@ -190,7 +191,7 @@ filterSample <- function() {
       inline = TRUE,
       choices = c(
         "Sample" = "sample",
-        sample_variables(physeq(), errorIfNULL = FALSE)
+        sample_variables(raw_physeq(), errorIfNULL = FALSE)
       ),
       selected = "sample"
     ),
@@ -211,10 +212,10 @@ output$filterUI <- renderUI({
   
   if (input$filterCriteria == "sample") {
     label <- "Sample to keep :"
-    choices <- sample_names(physeq())
+    choices <- sample_names(raw_physeq())
   } else {
     label <- "Variable to keep :"
-    choices <- levels(get_variable(physeq(), input$filterCriteria))
+    choices <- levels(get_variable(raw_physeq(), input$filterCriteria))
   }
   
   observe({
@@ -250,16 +251,18 @@ observeEvent(input$selectData, {
   } else {
     try(
       if (input$filterCriteria == "sample") {
-        physeq(prune_samples(samples = input$filterCheck, physeq()))
+        raw_physeq(prune_samples(samples = input$filterCheck, raw_physeq()))
       } else {
         criteria <<- input$filterCriteria
         check <<- input$filterCheck
-        physeq(subset_samples(physeq(), eval(parse(text = criteria)) %in% check))
+        raw_physeq(subset_samples(raw_physeq(), eval(parse(text = criteria)) %in% check))
         },
       silent = TRUE,
       outFile = showModal(dataInput(failed = TRUE)))
     
-    if (inherits(physeq(), "phyloseq")) {
+    if (inherits(raw_physeq(), "phyloseq")) {
+      message <- paste(input$filterCheck, collapse = ", ")
+      message(paste("[Easy16S] Select some samples :", message))
       removeModal()
     } else {
       showModal(dataInput(failed = TRUE))
@@ -275,9 +278,8 @@ transformSample <- function() {
     radioButtons(
       inputId = "transformFun",
       label = "Transform function : ",
-      selected = "none",
-      choices = c("None" = "none", 
-                  "Proportional Transformation" = "prop", 
+      selected = NULL,
+      choices = c("Proportional Transformation" = "prop", 
                   "Square Root Transformation" = "sqrt", 
                   "Square Root Proportional Transformation" = "sqrtprop", 
                   "Centered Log-Ratio (CLR) Transformation" = "clr")
@@ -286,7 +288,6 @@ transformSample <- function() {
     wellPanel(verbatimTextOutput("transformFun")),
     
     footer = tagList(modalButton("Cancel"),
-                     actionButton(inputId = "okData", label = "Refresh transformation"),
                      actionButton(inputId = "transformData", label = "Transforme")
     )
   )
@@ -295,7 +296,6 @@ transformSample <- function() {
 output$transformFun <- renderText({
   validate(need(input$transformFun, ""))
   switch (input$transformFun,
-          "none" = "",
           "prop" = paste("count_to_prop <- function(x) {return( x / sum(x) )}", 
                          "data_prop <- transform_sample_counts(data, count_to_prop)",
                          sep = "\n"),
@@ -321,19 +321,19 @@ observeEvent(input$transformData, {
   {
     removeModal()
   } else {
+    shinyWidgets::updateSwitchInput(session = session, inputId = "useTransf", value = FALSE)
     try(
       switch (input$transformFun,
-              "none" = {return(physeq())},
               "prop" = {
                 count_to_prop <- function(x) {return( x / sum(x) )}
-                physeq(transform_sample_counts(physeq(), count_to_prop))
+                transform_physeq(transform_sample_counts(raw_physeq(), count_to_prop))
               },
               "sqrt" = {
-                physeq(transform_sample_counts(physeq(), sqrt))
+                transform_physeq(transform_sample_counts(raw_physeq(), sqrt))
               },
               "sqrtprop" = {
                 count_to_sqrtprop <- function(x) {return(sqrt(x / sum(x)))}
-                physeq(transform_sample_counts(physeq(), count_to_sqrtprop))
+                transform_physeq(transform_sample_counts(raw_physeq(), count_to_sqrtprop))
               },
               "clr" = {
                 gm_mean <- function(x, na.rm=TRUE) {
@@ -344,20 +344,30 @@ observeEvent(input$transformData, {
                   x <- log(x/gm_mean(x), base)
                   return(x)
                 }
-                physeq(transform_sample_counts(physeq(), clr))
+                transform_physeq(transform_sample_counts(raw_physeq(), clr))
               }
       ),
       silent = TRUE,
       outFile = showModal(dataInput(failed = TRUE)))
     
-    if (class(physeq()) == "phyloseq") {
+    if (class(transform_physeq()) == "phyloseq") {
+      message(paste("[Easy16S] Transfom data :", input$transformFun))
+      shinyWidgets::updateSwitchInput(session = session, inputId = "useTransf", value = TRUE)
       removeModal()
     } else {
       showModal(dataInput(failed = TRUE))
-    }    
+    }
   }
 })
 
+observeEvent(input$useTransf,
+             if (input$useTransf) {
+               physeq(transform_physeq())
+             } else {
+               physeq(raw_physeq())
+             }
+             )
+
 ### Download Data ###
 dataDownload <- function() {
   modalDialog(

server.R

@@ -27,7 +27,9 @@ shinyServer
   source("panels/tree-server.R", local = TRUE)
 
   physeq <- reactiveVal()
-
+  raw_physeq <- reactiveVal()
+  transform_physeq <- reactiveVal()
+  
   showModal(dataInput())
 
   observeEvent(input$dataButton, {

ui.R

@@ -28,6 +28,13 @@ dashboardHeader(title = "Easy16S"),
                    "Transform abundance", 
                    icon = icon("square-root-alt"),
                    style = "width: 80% ; color: black ; background-color: gray90"),
+      shinyWidgets::switchInput("useTransf",
+                                value = FALSE,
+                                label = "Transformed Data",
+                                #inline = TRUE,
+                                size = "mini",
+                                labelWidth = "100%"
+                                ),
       actionButton("downloadButton", 
                    "Download data", 
                    icon = icon("download"),