plot_tree

server.R

@@ -111,7 +111,6 @@ shinyServer
   output$rarefactionMin <- renderText({
     if (!is.null(input$fileBiom)) {
       paste("(min sample =", format(min(sample_sums(data16S(
-        
       ))), big.mark = " "), "reads)")
     } else {
       paste("(min sample =", 0, "reads)")
@@ -729,16 +728,9 @@ shinyServer
       radioButtons(
         "treeRank",
         label = "Niveau taxonomique légendé :",
-        choices = list(
+        choices = c(
           aucun = "",
-          # rank_names(data16S()),
-          "Kingdom",
-          "Phylum",
-          "Class",
-          "Order",
-          "Family",
-          "Genus",
-          "Species",
+          rank_names(data16S()),
           OTU = "taxa_names"
         ),
         inline = TRUE
@@ -751,6 +743,7 @@ shinyServer
         value = 20
       ),
       checkboxInput("treeRadial", label = "Arbre radial", value = FALSE),
+      checkboxInput("treeSample", label = "Show samples", value = TRUE),
       if (!is.null(input$fileMeta)) {
         selectInput(
           "treeCol",
@@ -779,11 +772,12 @@ shinyServer
       physeq = prune_taxa(names(sort(
         taxa_sums(data16S()), decreasing = TRUE
       )[1:input$treeTopOtu]), data16S()),
+      method = ifelse(input$treeSample, "sampledodge", "treeonly"),
       color = checkNull(input$treeCol),
       shape = checkNull(input$treeShape),
       size = "abundance",
       label.tips = checkNull(input$treeRank),
-      sizebase = 2,
+      sizebase = 5,
       ladderize = "left",
       plot.margin = 0
     )