treeScript

server.R

@@ -1044,7 +1044,7 @@ shinyServer
   })
   
   output$treeUI <- renderUI({
-    validate(need(data16S(), ""))
+    validate(need(phy_tree(data16S(), errorIfNULL = FALSE), ""))
     box(
       title = "Setting : " ,
       width = NULL,
@@ -1078,8 +1078,52 @@ shinyServer
         "treeShape",
         label = "Shape : ",
         choices = c("..." = 0, sample_variables(data16S()))
+      ),
+      collapsedBox(verbatimTextOutput("treeScript"), title = "RCode")
+    )
+  })
+  
+  output$treeScript <- renderText({
+    scriptArgs <- c(
+      glue(
+        "physeq = prune_taxa(names(sort(taxa_sums(data), decreasing = TRUE)[1:{input$treeTopOtu}]), data)"
       )
     )
+    if (input$treeSample) {
+      scriptArgs <- c(scriptArgs, "method = \"sampledodge\"")
+    } else {
+      scriptArgs <- c(scriptArgs, "method = \"treeonly\"")
+    }
+    if (!is.null(checkNull(input$treeCol))) {
+      scriptArgs <- c(scriptArgs, glue("color = \"{input$treeCol}\""))
+    }
+    if (!is.null(checkNull(input$treeShape))) {
+      scriptArgs <- c(scriptArgs, glue("shape = \"{input$treeShape}\""))
+    }
+    scriptArgs <- c(scriptArgs, "size = \"abundance\"")
+    if (!is.null(checkNull(input$treeRank))) {
+      scriptArgs <-
+        c(scriptArgs, glue("label.tips = \"{input$treeRank}\""))
+    }
+    scriptArgs <- c(scriptArgs,
+                    "sizebase = 5",
+                    "ladderize = \"left\"",
+                    "plot.margin = 0")
+    if (!is.null(checkNull(input$treeTitle))) {
+      scriptArgs <- c(scriptArgs, glue("title = \"{input$treeTitle}\""))
+    }
+    script <- c(
+      scriptHead,
+      "# Plot phylogenetic tree",
+      glue("p <- plot_tree({glue_collapse(scriptArgs, sep=', ')})")
+    )
+    if (input$treeRadial) {
+      script <- c(script,
+                  "p <- p + coord_polar(theta = \"y\")")
+    }
+    script <- c(script, "", "plot(p)")
+    
+    return(glue_collapse(script, sep = "\n"))
   })
   
   output$tree <- renderPlot({