rework barplot with shinymeta

panels/barplot-server.R

 output$barplotShowRankUI <- renderUI({
-  validate(need(data16S(), ""))
+  validate(need(physeq(), ""))
   radioButtons(
     "barplotShowRank",
     label = "Taxonomic rank used for coloring : ",
-    choices = c(rank_names(data16S()), "OTU"),
+    choices = c(rank_names(physeq()), "OTU"),
     selected = "Phylum",
     inline = TRUE
   )
 })
 
 output$barplotFilterRankUI <- renderUI({
-  validate(need(data16S(), ""))
+  validate(need(physeq(), ""))
   radioButtons(
     "barplotFilterRank",
     label = "Taxonomic rank used for filtering : ",
-    choices = c("NULL" = 0, rank_names(data16S())),
+    choices = c("NULL" = 0, rank_names(physeq())),
     inline = TRUE
   )
 })
 
 output$barplotTaxaUI <- renderUI({
-  validate(need(data16S(), ""),
+  validate(need(physeq(), ""),
            need(input$barplotFilterRank, ""),
            need(input$barplotFilterRank!=0, ""))
   selectInput(
     "barplotTaxa",
     label = "Selected filter taxa : ",
-    choices = unique(as.vector(tax_table(data16S())[, input$barplotFilterRank])),
+    choices = unique(as.vector(tax_table(physeq())[, input$barplotFilterRank])),
     selected = TRUE
   )
 })
 
 output$barplotNbTaxaUI <- renderUI({
-  validate(need(data16S(), ""))
+  validate(need(physeq(), ""))
   sliderInput(
     "barplotNbTaxa",
     label = "Number of sub-taxa : ",
     min = 1,
-    #max = sum(tax_table(tax_glom(data16S(), rank_names(data16S())[1+as.integer(input$barplotFilterRank)]))[, as.integer(input$barplotFilterRank)]==input$barplotTaxa)
+    #max = sum(tax_table(tax_glom(physeq(), rank_names(physeq())[1+as.integer(input$barplotFilterRank)]))[, as.integer(input$barplotFilterRank)]==input$barplotTaxa)
     max = 30,
     value = 10
   )
 })
 
 output$barplotGridUI <- renderUI({
-  validate(need(data16S(), ""))
+  validate(need(physeq(), ""))
   selectInput("barplotGrid",
               label = "Subplot : ",
-              choices = c("..." = 0, sample_variables(data16S())))
+              choices = c("..." = 0, sample_variables(physeq())))
 })
 
 output$barplotXUI <- renderUI({
-  validate(need(data16S(), ""))
+  validate(need(physeq(), ""))
   selectInput("barplotX",
               label = "X : ",
-              choices = c("..." = 0, sample_variables(data16S())))
+              choices = c("..." = "Sample", sample_variables(physeq())))
 })
 
 output$barplotUI <- renderUI({
-  validate(need(data16S(), ""))
+  validate(need(physeq(), ""))
   box(
     title = "Setting : ",
     width = NULL,
@@ -68,57 +68,41 @@ output$barplotUI <- renderUI({
     uiOutput("barplotTaxaUI"),
     uiOutput("barplotNbTaxaUI"),
     uiOutput("barplotGridUI"),
-    uiOutput("barplotXUI"),
-    collapsedBox(verbatimTextOutput("barplotScript"), title = "RCode")
+    uiOutput("barplotXUI")
   )
 })
 
-output$barplotScript <- renderText({
-  scriptArgs <- c(
-    "physeq = data",
-    glue("taxaRank1 = \"{input$barplotFilterRank}\""),
-    glue("taxaSet1 = \"{input$barplotTaxa}\""),
-    glue("taxaRank2 = \"{input$barplotShowRank}\""),
-    glue("numberOfTaxa = {input$barplotNbTaxa}")
-  )
-  if (!is.null(checkNull(input$barplotX))) {
-    scriptArgs <- c(scriptArgs, glue("x = \"{input$barplotX}\""))
+output$barplot <- metaRender2(renderPlot, {
+  validate(need(physeq(), "Requires an abundance dataset"),
+           need(input$barplotShowRank, ""))
+  
+  barplotGrid <- if (!is.null(checkNull(input$barplotGrid))) {
+    metaExpr({
+      facet_grid(..(paste(".", "~", input$barplotGrid)), scales = "free_x")
+    })
   }
-  script <- c(
-    scriptHead,
-    "# Plot filtered barplot",
-    glue(
-      "p <- plot_composition({glue_collapse(scriptArgs, sep=', ')})"
-    )
-  )
-  if (!is.null(checkNull(input$barplotGrid))) {
-    script <- c(
-      script,
-      glue(
-        "p <- p + facet_grid(\". ~ {input$barplotGrid}\", scales = \"free_x\")"
-      )
+  
+  metaExpr({
+    p <- plot_composition(
+      physeq = physeq(),
+      taxaRank1 = ..(checkNull(input$barplotFilterRank)),
+      taxaSet1 = ..(input$barplotTaxa),
+      taxaRank2 = ..(input$barplotShowRank),
+      numberOfTaxa = ..(input$barplotNbTaxa),
+      x = ..(input$barplotX)
     )
-  }
-  script <- c(script, "", "plot(p)")
-
-  return(glue_collapse(script, sep = "\n"))
+    p + ..(barplotGrid)
+  })
 })
 
-output$barplot <- renderPlot({
-  validate(
-    need(data16S(), "Requires an abundance dataset"),
-    need(input$barplotShowRank, "")
-  )
-  p <- plot_composition(
-    physeq = data16S(),
-    taxaRank1 = checkNull(input$barplotFilterRank),
-    taxaSet1 = input$barplotTaxa,
-    taxaRank2 = input$barplotShowRank,
-    numberOfTaxa = input$barplotNbTaxa,
-    x = ifelse(is.null(checkNull(input$barplotX)), "Sample", input$barplotX)
-  )
-  if (!is.null(checkNull(input$barplotGrid))) {
-    p <- p + facet_grid(paste(".", "~", input$barplotGrid), scales = "free_x")
-  }
-  return(p)
-})
+observeEvent(input$barplot_output_code,
+             {
+               displayCodeModal(
+                 expandChain(
+                   quote(library(phyloseq)),
+                   quote(library(phyloseq.extended)),
+                   output$barplot()
+                 )
+               )
+             }
+)

panels/barplot-ui.R

-barplot <-fluidPage(withLoader(plotOutput("barplot", height = 700)),
-                      uiOutput("barplotUI"))
+barplot <-fluidPage(outputCodeButton(withLoader(plotOutput("barplot", height = 700))),
+                    uiOutput("barplotUI"))

server.R

 options(shiny.maxRequestSize = 30 * 1024 ^ 2)
 
 library(shinydashboard)
+library(shinymeta)
 library(phyloseq)
 library(phyloseq.extended)
 library(ggplot2)

ui.R

 library(shinydashboard)
+library(shinymeta)
 library(shinycustomloader)
 source("panels/Summary-ui.R", local = TRUE)
 source("panels/barplot-ui.R", local = TRUE)