upload RData

server.R

@@ -27,7 +27,7 @@ shinyServer
       options = list(
         dom = "lBtip",
         pageLength = 10,
-        lengthMenu = list(c(10, 25, 50, 100, -1), list('10', '25', '50', '100', 'All')),
+        lengthMenu = list(c(10, 25, 50, 100,-1), list('10', '25', '50', '100', 'All')),
         buttons = list(
           'colvis',
           list(
@@ -50,12 +50,8 @@ shinyServer
   })
   
   data16S <- reactive({
-    if (input$demo != "input")
+    if (input$dataset == "input")
     {
-      load("demo/demo.RData")
-      return(get(input$demo))
-    }
-    else {
       if (is.null(input$fileBiom))
       {
         return()
@@ -116,11 +112,19 @@ shinyServer
         )
       }
       return(d)
+    } else if (input$dataset == "rdata")
+    {
+      load(input$fileRData$datapath)
+      return(data)
+    } else {
+      load("demo/demo.RData")
+      return(get(input$dataset))
     }
   })
   
   output$rarefactionMin <- renderText({
-    validate(need(input$fileBiom, ""), need(input$demo == "input", ""))
+    validate(need(input$fileBiom, ""),
+             need(input$dataset == "input", ""))
     paste("(min sample =", format(min(sample_sums(data16S(
       
     ))), big.mark = " "), "reads)")

ui.R

@@ -6,15 +6,25 @@ shinyUI(dashboardPage(
     tags$div(
       title = "Select dataset for demonstration",
       selectInput(
-        "demo",
-        label = "Select demo dataset : ",
-        choices = list("Input data" = "input",
-                       "Chaillou et al., 2015" = "food"),
+        "dataset",
+        label = "Select dataset : ",
+        choices = list(
+          "Input data" = "input",
+          "Rdata" = "rdata",
+          "Demo : Chaillou et al., 2015" = "food"
+        ),
         # "Mach et al., 2015" = "kinetic", "Morton et al., 2017" = "soil", "Ravel et al., 2011" = "ravel", "biorare" = "biorare", "GlobalPatterns" = "GlobalPatterns"
         selected = 1
       )
     ),
-    hr(width = "90%"),
+    hr(),
+    tags$div(
+      title = "RData where 'data' is a phyloseq object.",
+      fileInput("fileRData",
+                label = "RData : ",
+                placeholder = "data.RData")
+    ),
+    hr(),
     tags$div(
       title = "Abundance BIOM file come from FROGS with 'FROGS BIOM to std BIOM', Qiime or another metagenomic tool.",
       fileInput("fileBiom",