fonctions dans internals.R

internals.R

@@ -59,3 +59,72 @@
   ## Unhappy paths: everything else
   return()
 }
+
+###
+
+checkNull <- function(x) {
+  if (!exists(as.character(substitute(x)))) {
+    return(NULL)
+  } else if (is.null(x)) {
+    return(NULL)
+  } else if (length(x) > 1) {
+    return(x)
+  }
+  else if (x %in% c(0, "", NA, "NULL")) {
+    return(NULL)
+  } else {
+    return(x)
+  }
+}
+
+beautifulTable <- function(data)  {
+  DT::datatable(
+    data = data,
+    rownames = FALSE,
+    filter = "top",
+    extensions = c("Buttons", "ColReorder", "FixedColumns"),
+    options = list(
+      dom = "lBtip",
+      pageLength = 10,
+      lengthMenu = list(c(10, 25, 50, 100,-1), list('10', '25', '50', '100', 'All')),
+      buttons = list(
+        'colvis',
+        list(
+          extend = 'collection',
+          buttons = c('copy', 'csv', 'excel', 'pdf'),
+          text = 'Download'
+        )
+      ),
+      colReorder = TRUE,
+      scrollX = TRUE,
+      fixedColumns = list(leftColumns = 1, rightColumns = 0)
+    ),
+    width = "auto",
+    height = "auto"
+  )
+}
+
+collapsedBox <- function(data, title = title)  {
+  box(
+    title = title,
+    width = NULL,
+    status = "primary",
+    collapsible = TRUE,
+    collapsed = TRUE,
+    data
+  )
+}
+
+scriptHead <- c(
+  "# Loading packages",
+  "library(phyloseq.extended)",
+  "",
+  "# Loading data",
+  glue(
+    "load(\"Easy16S-data.{Sys.Date()}.RData\") # if necessary, adapt the file path"
+  ),
+  "",
+  "# View data",
+  "data",
+  ""
+)

server.R

@@ -10,7 +10,9 @@ library(factoextra)
 
 shinyServer
 (function(input, output, session)
-{
+{  
+  source("internals.R")
+  source("panels/dataInput.R", local = TRUE)
   source("panels/Sidebar-server.R", local = TRUE)
   source("panels/Summary-server.R", local = TRUE)
   source("panels/barplot-server.R", local = TRUE)
@@ -23,61 +25,6 @@ shinyServer
   source("panels/tree-server.R", local = TRUE)
   source("panels/cluster-server.R", local = TRUE)
   
-  checkNull <- function(x) {
-    if (!exists(as.character(substitute(x)))) {
-      return(NULL)
-    } else if (is.null(x)) {
-      return(NULL)
-    } else if (length(x) > 1) {
-      return(x)
-    }
-    else if (x %in% c(0, "", NA, "NULL")) {
-      return(NULL)
-    } else {
-      return(x)
-    }
-  }
-  
-  beautifulTable <- function(data)  {
-    DT::datatable(
-      data = data,
-      rownames = FALSE,
-      filter = "top",
-      extensions = c("Buttons", "ColReorder", "FixedColumns"),
-      options = list(
-        dom = "lBtip",
-        pageLength = 10,
-        lengthMenu = list(c(10, 25, 50, 100,-1), list('10', '25', '50', '100', 'All')),
-        buttons = list(
-          'colvis',
-          list(
-            extend = 'collection',
-            buttons = c('copy', 'csv', 'excel', 'pdf'),
-            text = 'Download'
-          )
-        ),
-        colReorder = TRUE,
-        scrollX = TRUE,
-        fixedColumns = list(leftColumns = 1, rightColumns = 0)
-      ),
-      width = "auto",
-      height = "auto"
-    )
-  }
-  
-  collapsedBox <- function(data, title = title)  {
-    box(
-      title = title,
-      width = NULL,
-      status = "primary",
-      collapsible = TRUE,
-      collapsed = TRUE,
-      data
-    )
-  }
-  
-  source("internals.R")
-  
   data16S <- reactive({
     ## BIOM input
     if (input$dataset == "input")
@@ -138,18 +85,4 @@ shinyServer
         isolate(data <<- data16S())
     })
   }
-  
-  scriptHead <- c(
-    "# Loading packages",
-    "library(phyloseq.extended)",
-    "",
-    "# Loading data",
-    glue(
-      "load(\"Easy16S-data.{Sys.Date()}.RData\") # if necessary, adapt the file path"
-    ),
-    "",
-    "# View data",
-    "data",
-    ""
-  )
 })

ui.R

@@ -14,8 +14,9 @@ source("panels/cluster-ui.R", local = TRUE)
 source("panels/Help-ui.R", local = TRUE)
 
 shinyUI(dashboardPage(
-  dashboardHeader(title = "Easy16S"),
+dashboardHeader(title = "Easy16S"),
   dashboardSidebar(
+      actionButton("dataButton", "Select your data"),
     sidebarMenu(
       menuItem("Data", tabName = "Data", icon = icon("dashboard")),
       menuItem("Summary", tabName = "Summary", icon = icon("dashboard")),