networkBScript + heatmapScript

server.R

@@ -578,8 +578,11 @@ shinyServer
     script <- c(script, "", "# Tables")
     script <- c(
       script,
-      glue("t <- estimate_richness({glue_collapse(c(\"data\", measures), sep=', ')})"),
-      "write.table(t, file = \"richness.tsv\", sep = \"\\t\", col.names = NA)")
+      glue(
+        "t <- estimate_richness({glue_collapse(c(\"data\", measures), sep=', ')})"
+      ),
+      "write.table(t, file = \"richness.tsv\", sep = \"\\t\", col.names = NA)"
+    )
     
     return(glue_collapse(script, sep = "\n"))
   })
@@ -660,10 +663,12 @@ shinyServer
       script <- c(script, "tipColor <- NULL")
     }
     script <-
-      c(script,
+      c(
+        script,
         "",
         "p1 <- ggplot(beta, aes(x = x, y = y, fill = distance))",
-        "p1 <- p1 + geom_tile()")
+        "p1 <- p1 + geom_tile()"
+      )
     if (!is.null(checkNull(input$richnessBTitle))) {
       script <- c(script,
                   glue("p1 <- p1 + ggtitle(\"{input$richnessBTitle}\")"))
@@ -755,8 +760,38 @@ shinyServer
           "Sample name" = "value",
           sample_variables(data16S())
         )
-      )
+      ),
+      collapsedBox(verbatimTextOutput("networkBScript"), title = "RCode")
+    )
+  })
+  
+  output$networkBScript <- renderText({
+    scriptArgs <- c("g",
+                    "physeq = data",
+                    "hjust = 2")
+    if (!is.null(checkNull(input$netwCol))) {
+      scriptArgs <- c(scriptArgs, glue("color = \"{input$netwCol}\""))
+    }
+    if (!is.null(checkNull(input$netwShape))) {
+      scriptArgs <- c(scriptArgs, glue("shape = \"{input$netwShape}\""))
+    }
+    if (!is.null(checkNull(input$netwLabel))) {
+      scriptArgs <- c(scriptArgs, glue("label = \"{input$netwLabel}\""))
+    }
+    if (!is.null(checkNull(input$netwTitle))) {
+      scriptArgs <- c(scriptArgs, glue("title = \"{input$netwTitle}\""))
+    }
+    script <- c(
+      scriptHead,
+      "# Plot samples network",
+      glue(
+        "g <- make_network(data, distance = \"{input$richnessBDist}\", max.dist = {input$netwMax}, keep.isolates = {input$netwOrphan})"
+      ),
+      glue("p <- plot_network({glue_collapse(scriptArgs, sep=', ')})")
     )
+    script <- c(script, "", "plot(p)")
+    
+    return(glue_collapse(script, sep = "\n"))
   })
   
   output$networkB <- renderPlot({
@@ -942,8 +977,48 @@ shinyServer
           "median",
           "centroid"
         )
+      ),
+      collapsedBox(verbatimTextOutput("heatmapScript"), title = "RCode")
+    )
+  })
+  
+  output$heatmapScript <- renderText({
+    scriptArgs <-
+      c(
+        glue(
+          "prune_taxa(names(sort(taxa_sums(data), decreasing = TRUE)[1:{input$heatmapTopOtu}]), data)"
+        ),
+        glue("distance = \"{input$heatmapDist}\""),
+        glue("method = \"{input$heatmapMethod}\""),
+        "low = \"yellow\"",
+        "high = \"red\"",
+        "na.value = \"white\""
       )
+    if (!is.null(checkNull(input$heatmapX))) {
+      scriptArgs <-
+        c(scriptArgs, glue("sample.order = \"{input$heatmapX}\""))
+    }
+    if (!is.null(checkNull(input$heatmapTitle))) {
+      scriptArgs <-
+        c(scriptArgs, glue("title = \"{input$heatmapTitle}\""))
+    }
+    
+    script <- c(
+      scriptHead,
+      "# Plot heatmap",
+      glue("p <- plot_heatmap({glue_collapse(scriptArgs, sep=', ')})")
     )
+    if (!is.null(checkNull(input$heatmapGrid))) {
+      script <- c(
+        script,
+        glue(
+          "p <- p + facet_grid(\". ~ {input$heatmapGrid}\", scales = \"free_x\")"
+        )
+      )
+    }
+    script <- c(script, "", "plot(p)")
+    
+    return(glue_collapse(script, sep = "\n"))
   })
   
   output$Heatmap <- renderPlot({