From d462227a85025774ade5e8f67b1edff72d7f8e4a Mon Sep 17 00:00:00 2001
From: Cedric Midoux <cedric.midoux@inra.fr>
Date: Tue, 11 Sep 2018 11:16:59 +0200
Subject: [PATCH] histFocusScript

---
 server.R | 63 +++++++++++++++++++++++++++++++++++++++++++++++++++-----
 ui.R     | 13 ++----------
 2 files changed, 60 insertions(+), 16 deletions(-)

diff --git a/server.R b/server.R
index cf4a028..21f8e84 100644
--- a/server.R
+++ b/server.R
@@ -28,7 +28,7 @@ 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(
@@ -293,7 +293,8 @@ shinyServer
   })
   
   output$histFocusUIfocusTaxa <- renderUI({
-    validate(need(data16S(), ""))
+    validate(need(data16S(), ""),
+             need(input$focusRank, ""))
     selectInput(
       "focusTaxa",
       label = "Selected taxa : ",
@@ -330,9 +331,61 @@ shinyServer
                 choices = c("..." = 0, sample_variables(data16S())))
   })
   
-  output$histoFocus <- renderPlot({
-    validate(need(data16S(),
-                  "Requires an abundance dataset"))
+  output$histFocusUI <- renderUI({
+    validate(need(data16S(), ""))
+    box(
+      title = "Setting : ",
+      width = NULL,
+      status = "primary",
+      uiOutput("histFocusUIfocusRank"),
+      uiOutput("histFocusUIfocusTaxa"),
+      uiOutput("histFocusUIfocusNbTaxa"),
+      uiOutput("histFocusUIfocusGrid"),
+      uiOutput("histFocusUIfocusX"),
+      collapsedBox(verbatimTextOutput("histFocusScript"), title = "RCode")
+    )
+  })
+  
+  output$histFocusScript <- renderText({
+    paste0(
+      scriptHead,
+      "# Plot filtered barplot\n",
+      "p <- plot_composition(physeq = data",
+      glue(", taxaRank1 = \"{input$focusRank}\""),
+      glue(", taxaSet1 = \"{input$focusTaxa}\""),
+      glue(
+        ", taxaRank2 = \"{rank_names(data16S())[which(rank_names(data16S()) == input$focusRank) + 1]}\""
+      ),
+      glue(", numberOfTaxa = {input$focusNbTaxa}"),
+      glue(
+        ", fill = \"{rank_names(data16S())[which(rank_names(data16S()) == input$focusRank) + 1]}\""
+      ),
+      ifelse(is.null(checkNull(input$focusX)),
+             "",
+             glue(", x = \"{input$focusX}\"")),
+      ")\n",
+      ifelse(
+        is.null(checkNull(input$focusGrid)),
+        "",
+        glue(
+          "p <- p + facet_grid(\". ~ {input$focusGrid}\", scales = \"free_x\")"
+        )
+      ),
+      ###
+      #  x = ifelse(is.null(checkNull(input$focusX)), "Sample", input$focusX)
+      ###
+      "\n",
+      "plot(p)"
+    )
+  })
+  
+  output$histFocus <- renderPlot({
+    validate(
+      need(data16S(),
+           "Requires an abundance dataset"),
+      need(input$focusRank, ""),
+      need(input$focusTaxa, "")
+    )
     p <- plot_composition(
       physeq = data16S(),
       taxaRank1 = input$focusRank,
diff --git a/ui.R b/ui.R
index cd24170..94de056 100644
--- a/ui.R
+++ b/ui.R
@@ -104,17 +104,8 @@ shinyUI(dashboardPage(
                uiOutput("histUI")),
       tabPanel(
         "Filtered barplot",
-        withLoader(plotOutput("histoFocus", height = 700)),
-        box(
-          title = "Paramètres",
-          width = NULL,
-          status = "primary",
-          uiOutput("histFocusUIfocusRank"),
-          uiOutput("histFocusUIfocusTaxa"),
-          uiOutput("histFocusUIfocusNbTaxa"),
-          uiOutput("histFocusUIfocusGrid"),
-          uiOutput("histFocusUIfocusX")
-        )
+        withLoader(plotOutput("histFocus", height = 700)),
+        uiOutput("histFocusUI")
       ),
       tabPanel("Heatmap",
                withLoader(plotOutput("Heatmap", height = 700)),
-- 
2.26.2