Start the interface for raw data push

LoadPackages.R

@@ -164,18 +164,4 @@ if(!require(PhyloTreeMetaR)){
 #   library(plotly)  
 # }
 
-# Allow to upload 50M files only shaman server
-if(Sys.info()["nodename"] == "ShinyPro"){
-  options(shiny.maxRequestSize=50*1024^2)
-}else{
-  # No limit
-  options(shiny.maxRequestSize=500000000000000*1024^2)
-}
-source("Rfunctions/Data_Management.R")
-source("Rfunctions/Stat_Model.R")
-source("Rfunctions/DiagPlot.R")
-source("Rfunctions/VisuPlot.R")
-source("Rfunctions/CompPlot.R")
-source("Rfunctions/DiffTable.R")
-
 

Rfunctions/directoryInput.R

+#' Choose a Folder Interactively (Mac OS X)
+#'
+#' Display a folder selection dialog under Mac OS X
+#'
+#' @param default which folder to show initially
+#' @param caption the caption on the selection dialog
+#'
+#' @details
+#' Uses an Apple Script to display a folder selection dialog.  With \code{default = NA},
+#' the initial folder selection is determined by default behavior of the
+#' "choose folder" Apple Script command.  Otherwise, paths are expanded with
+#' \link{path.expand}.
+#'
+#' @return
+#' A length one character vector, character NA if 'Cancel' was selected.
+#'
+if (Sys.info()['sysname'] == 'Darwin') {
+  choose.dir = function(default = NA, caption = NA) {
+    command = 'osascript'
+    args = '-e "POSIX path of (choose folder{{prompt}}{{default}})"'
+
+    if (!is.null(caption) && !is.na(caption) && nzchar(caption)) {
+      prompt = sprintf(' with prompt \\"%s\\"', caption)
+    } else {
+      prompt = ''
+    }
+    args = sub('{{prompt}}', prompt, args, fixed = T)
+
+    if (!is.null(default) && !is.na(default) && nzchar(default)) {
+      default = sprintf(' default location \\"%s\\"', path.expand(default))
+    } else {
+      default = ''
+    }
+    args = sub('{{default}}', default, args, fixed = T)
+
+    suppressWarnings({
+      path = system2(command, args = args, stderr = TRUE)
+    })
+    if (!is.null(attr(path, 'status')) && attr(path, 'status')) {
+      # user canceled
+      path = NA
+    }
+
+    return(path)
+  }
+} else if (Sys.info()['sysname'] == 'Linux') {
+  choose.dir = function(default = NA, caption = NA) {
+    command = 'zenity'
+    args = '--file-selection --directory --title="Choose a folder"'
+    
+    suppressWarnings({
+      path = system2(command, args = args, stderr = TRUE)
+    })
+    
+    #Return NA if user hits cancel
+    if (!is.null(attr(path, 'status')) && attr(path, 'status')) {
+      # user canceled
+      return(default)
+    }
+    
+    #Error: Gtk-Message: GtkDialog mapped without a transient parent
+    if(length(path) == 2){
+      path = path[2]
+    }
+    
+    return(path)
+  }
+}
+
+#' Directory Selection Control
+#'
+#' Create a directory selection control to select a directory on the server
+#'
+#' @param inputId The \code{input} slot that will be used to access the value
+#' @param label Display label for the control, or NULL for no label
+#' @param value Initial value.  Paths are exapnded via \code{\link{path.expand}}.
+#'
+#' @details
+#' This widget relies on \link{\code{choose.dir}} to present an interactive
+#' dialog to users for selecting a directory on the local filesystem.  Therefore,
+#' this widget is intended for shiny apps that are run locally - i.e. on the
+#' same system that files/directories are to be accessed - and not from hosted
+#' applications (e.g. from shinyapps.io).
+#'
+#' @return
+#' A directory input control that can be added to a UI definition.
+#'
+#' @seealso
+#' \link{updateDirectoryInput}, \link{readDirectoryInput}, \link[utils]{choose.dir}
+directoryInput = function(inputId, label, value = NULL) {
+  if (!is.null(value) && !is.na(value)) {
+    value = path.expand(value)
+  }
+
+  tagList(
+    singleton(
+      tags$head(
+        tags$script(src = 'js/directory_input_binding.js')
+      )
+    ),
+
+    div(
+      class = 'form-group directory-input-container',
+      shiny:::`%AND%`(label, tags$label(label)),
+      div(
+        span(
+          class = 'col-xs-9 col-md-11',
+          style = 'padding-left: 0; padding-right: 5px;',
+          div(
+            class = 'input-group shiny-input-container',
+            style = 'width:100%;',
+            div(class = 'input-group-addon', icon('folder-o')),
+            tags$input(
+              id = sprintf('%s__chosen_dir', inputId),
+              value = value,
+              type = 'text',
+              class = 'form-control directory-input-chosen-dir',
+              readonly = 'readonly'
+            )
+          )
+        ),
+        span(
+          class = 'shiny-input-container',
+          tags$button(
+            id = inputId,
+            class = 'btn btn-default directory-input',
+            '...'
+          )
+        )
+      )
+    )
+
+  )
+
+}
+
+#' Change the value of a directoryInput on the client
+#'
+#' @param session The \code{session} object passed to function given to \code{shinyServer}.
+#' @param inputId The id of the input object.
+#' @param value A directory path to set
+#' @param ... Additional arguments passed to \link{\code{choose.dir}}.  Only used
+#'    if \code{value} is \code{NULL}.
+#'
+#' @details
+#' Sends a message to the client, telling it to change the value of the input
+#' object.  For \code{directoryInput} objects, this changes the value displayed
+#' in the text-field and triggers a client-side change event.  A directory
+#' selection dialog is not displayed.
+#'
+updateDirectoryInput = function(session, inputId, value = NULL, ...) {
+  if (is.null(value)) {
+    value = choose.dir(...)
+  }
+  session$sendInputMessage(inputId, list(chosen_dir = value))
+}
+
+#' Read the value of a directoryInput
+#'
+#' @param session The \code{session} object passed to function given to \code{shinyServer}.
+#' @param inputId The id of the input object
+#'
+#' @details
+#' Reads the value of the text field associated with a \code{directoryInput}
+#' object that stores the user selected directory path.
+#'
+readDirectoryInput = function(session, inputId) {
+  session$input[[sprintf('%s__chosen_dir', inputId)]]
+}

global.R

+# Allow to upload 50M files only shaman server
+if(Sys.info()["nodename"] == "ShinyPro"){
+  options(shiny.maxRequestSize=50*1024^2)
+}else{
+  # No limit
+  options(shiny.maxRequestSize=500000000000000*1024^2)
+}
+
+
+source('LoadPackages.R')
+source("css/owncss.R")
+source("Rfunctions/Data_Management.R")
+source("Rfunctions/Stat_Model.R")
+source("Rfunctions/DiagPlot.R")
+source("Rfunctions/VisuPlot.R")
+source("Rfunctions/CompPlot.R")
+source("Rfunctions/DiffTable.R")
+source('Rfunctions/directoryInput.R')

server.R

-source('LoadPackages.R')
-
 shinyServer(function(input, output,session) {
 
   hide(id = "loading-content", anim = TRUE, animType = "fade",time=1.5)
@@ -10,6 +8,8 @@ shinyServer(function(input, output,session) {
   ##
   #####################################################
   
+  
+  
   ## Create base for contrast
   rand = floor(runif(1,0,1e9))
   namesfile = tempfile(pattern = "BaseContrast", tmpdir = tempdir(), fileext = "")
@@ -605,6 +605,25 @@ shinyServer(function(input, output,session) {
   })
   
   
+  ## Select a folder (for MASQUE)
+  observeEvent(
+    ignoreNULL = TRUE,
+    eventExpr = {
+      input$directory
+    },
+    handlerExpr = {
+      if (input$directory > 0) {
+        # condition prevents handler execution on initial app launch
+        
+        # launch the directory selection dialog with initial path read from the widget
+        path = choose.dir(default = readDirectoryInput(session, 'directory'))
+        
+        # update the widget value
+        updateDirectoryInput(session, 'directory', value = path)
+      }
+    }
+  )
+  
   observeEvent(input$deleteRows,{
     
     if (!is.null(input$DataTarget_rows_selected)) {

ui.R

-options(shiny.sanitize.errors = FALSE)
-source("css/owncss.R")
-source("Rfunctions/Data_Management.R")
-if (!require(devtools)) {
-  install.packages('devtools')
-  library(devtools)
-}
-if(!require(treeWeightD3)){
-  devtools::install_github('pierreLec/treeWeightD3')
-  library(treeWeightD3)
-}
-if (!require(scatterD3)) {
-  devtools::install_github('aghozlane/scatterD3')
-  library(scatterD3)
-}
-if(!require(shinydashboard)){
-  devtools::install_github('aghozlane/shinydashboard')
-  library(shinydashboard)
-}
-
-if(!require(shinythemes)){
-  install.packages("shinythemes")
-  library(shinythemes)
-}
-if(!require(shinyjs)){
-  install.packages("shinyjs")
-  library(shinyjs)  
-}
-
 function(request) {
 sidebar <- dashboardSidebar(
   useShinyjs(),
@@ -42,6 +13,7 @@ sidebar <- dashboardSidebar(
     menuItem("Home", tabName = "Home", icon = icon("home")),
     menuItem("Tutorial", tabName = "Tutorial", icon = icon("book")),
     menuItem("Download/Install", tabName = "Download", icon = icon("download")),
+    menuItem("Raw data", tabName = "RawData", icon = icon("upload")),
     menuItem("Upload your data", tabName = "Upload", icon = icon("upload")),
     # bookmarkButton(),
     menuItemOutput("dymMenu"),
@@ -248,7 +220,52 @@ body <- dashboardBody(
                      )
               )
             ),
-    
+    tabItem(tabName = "RawData",
+                        tags$style(type='text/css', ".well { max-width: 20em; }"),
+                        fluidRow(
+                          HTML('<center><h1>MASQUE : Metagenomic Analysis with a Quantitative pipeline</h1></center>'),
+
+                          column(width=8,
+                            div(style="background-color: white; padding-left:20px;",
+                            HTML('
+                           <h2>Introduction</h2>
+
+                                 <p>The aim of this part is to provide an easy cluster interface to perform <b>targeted metagenomic analysis</b>. This analysis will be done using the MASQUE pipeline which allows :</p>
+
+                                 <ul>
+                                 <li>to analyse 16S/18S/23S/28S/ITS data. It builds a count matrix, an annotation table and a phylogeny of the OTU.</li>
+                                 <li>to perform to use a set of parameters already tested on serveral projects for the numerous software used to perform the clustering and the annotation.</li>
+                                 <li>to perform an "uptodate" analysis considering the scientific litterature.</li>
+                                 </ul>
+
+                                  <hr></hr>
+                                 <h2>Process</h2>
+
+                                 <p>We follow the recommandation described by Robert C. Edgar in <a href="http://www.nature.com/nmeth/journal/v10/n10/full/nmeth.2604.html" target="_blank" >Uparse</a> supplementary paper.<br>
+                                   The clustering process in MASQUE is performed as the following :<br>
+                                   1.  Read quality control<br>
+                                   2.  Dereplication<br>
+                                   3.  Chimera filtering<br>
+                                   4.  Clustering<br>
+                                   5.  Realignment/mapping<br>
+                                   6.  Taxonomical annotation of the OTU<br>
+                                   7.  Quality check of every step  </p>
+
+                                   <p>You can find more information in the presentation <a href="/aghozlane/masque/blob/master/tp/Targeted_metagenomics.pdf">here</a>. We try to describe the idea behind each step and a complete TP to do it on your own.</p>'
+                              )
+            #
+            #
+            #                      <\ui> to analyse 16S/18S/23S/28S/ITS data. It builds a count matrix, an annotation table and a phylogeny of the OTU.
+            #                      to perform to use a set of parameters already tested on serveral projects for the numerous software used to perform the clustering and the annotation.
+            #                      to perform an uptodate analysis considering the scientific litterature."
+                          ))),
+                      fluidRow(directoryInput('directory', label = 'select a directory')),
+
+                        br(),
+                        fluidRow(
+                        )
+            ),
+
     tabItem(tabName = "Upload",
             tags$style(type='text/css', ".well { max-width: 20em; }"),
             fluidRow(