betaMDS

panels/mds-server.R

-output$mdsUI <- renderUI({
-  validate(need(physeq(), ""))
-  box(
-    title = "Setting : " ,
-    width = NULL,
-    status = "primary",
-    checkboxGroupInput(
-      "mdsAxes",
-      label = "Axes : ",
-      choices = seq(10),
-      selected = c(1, 2),
-      inline = TRUE
-    ),
-    selectInput(
-      "mdsDist",
-      label = "Distance : ",
-      selected = "bray",
-      choices = list(
-        "bray",
-        "jaccard",
-        "unifrac",
-        "wunifrac",
-        "dpcoa",
-        "jsd",
-        "euclidean"
-      )
-    ),
-    selectInput(
-      "mdsMethod",
-      label = "Method : ",
-      selected = "MDS",
-      choices = list("DCA (Detrended Correspondence Analysis)" = "DCA", 
-                     "CCA (Constrained Correspondence Analysis)" = "CCA", 
-                     "RDA (Redundancy Analysis)" = "RDA", 
-                     "CAP (Constrained Analysis of Principal Coordinates)" = "CAP", 
-                     "DPCoA (Double Principle Coordinate Analysis)" = "DPCoA", 
-                     "NMDS (Non-metric MultiDimenstional Scaling)" = "NMDS", 
-                     "MDS / PCoA (Principal Coordinate Analysis)" = "MDS")
-    ),
-    textInput("mdsTitle",
-              label = "Title : ",
-              value = "Samples ordination graphic"),
-    selectInput(
-      "mdsLabel",
-      label = "Label : ",
-      choices = c("..." = 0, sample_variables(physeq()))
-    ),
-    selectInput(
-      "mdsCol",
-      label = "Color : ",
-      choices = c("..." = 0, sample_variables(physeq()))
-    ),
-    selectInput(
-      "mdsShape",
-      label = "Shape : ",
-      choices = c("..." = 0, sample_variables(physeq()))
-    ),
-    selectInput(
-      "mdsEllipse",
-      label = "Ellipses : ",
-      choices = c("..." = 0, sample_variables(physeq()))
-    )
-  )
-})
-
-output$mds <- metaRender2(renderPlot, {
-  validate(need(physeq(), "Requires an abundance dataset"),
-           need(length(input$mdsAxes) == 2, "Requires two projections axes"))
-  data <- physeq()
-  
-  mdsEllipse <- if (!is.null(checkNull(input$mdsEllipse))) {
-    metaExpr({
-      stat_ellipse(aes_string(group = ..(input$mdsEllipse)))
-    })
-  }
-  
-  metaExpr({
-    ord <- ordinate(data,
-                    method = ..(input$mdsMethod),
-                    distance = ..(input$mdsDist))
-    p <- plot_ordination(
-      physeq = data,
-      ordination = ord,
-      type = "samples",
-      axes = ..(as.numeric(input$mdsAxes)),
-      color = ..(checkNull(input$mdsCol)),
-      shape = ..(checkNull(input$mdsShape)),
-      label = ..(checkNull(input$mdsLabel)),
-      title = ..(checkNull(input$mdsTitle))
-    )
-    p <- p + ..(mdsEllipse)
-    p + theme_bw()
-  })
-})
-
-observeEvent(input$mds_output_code,
-             {
-               displayCodeModal(
-                 expandChain(
-                   quote(library(phyloseq)),
-                   quote(library(phyloseq.extended)),
-                   "# Replace `data` with you own data.",
-                   output$mds()
-                 )
-               )
-             }
-)

panels/mds-ui.R

-mds <- fluidPage(outputCodeButton(withLoader(plotOutput("mds", height = 700))),
-                     uiOutput("mdsUI"))

panels/richnessB-server.R

+output$betaMdsUI <- renderUI({
+  validate(need(physeq(), ""))
+  box(
+    title = "Setting : " ,
+    width = NULL,
+    status = "primary",
+    checkboxGroupInput(
+      "betaMdsAxes",
+      label = "Axes : ",
+      choices = seq(10),
+      selected = c(1, 2),
+      inline = TRUE
+    ),
+    selectInput(
+      "betaMdsMethod",
+      label = "Method : ",
+      selected = "MDS",
+      choices = list("DCA (Detrended Correspondence Analysis)" = "DCA", 
+                     "CCA (Constrained Correspondence Analysis)" = "CCA", 
+                     "RDA (Redundancy Analysis)" = "RDA", 
+                     "CAP (Constrained Analysis of Principal Coordinates)" = "CAP", 
+                     "DPCoA (Double Principle Coordinate Analysis)" = "DPCoA", 
+                     "NMDS (Non-metric MultiDimenstional Scaling)" = "NMDS", 
+                     "MDS / PCoA (Principal Coordinate Analysis)" = "MDS")
+    ),
+    textInput("betaMdsTitle",
+              label = "Title : ",
+              value = "Samples ordination graphic"),
+    selectInput(
+      "betaMdsLabel",
+      label = "Label : ",
+      choices = c("..." = 0, sample_variables(physeq()))
+    ),
+    selectInput(
+      "betaMdsCol",
+      label = "Color : ",
+      choices = c("..." = 0, sample_variables(physeq()))
+    ),
+    selectInput(
+      "betaMdsShape",
+      label = "Shape : ",
+      choices = c("..." = 0, sample_variables(physeq()))
+    ),
+    selectInput(
+      "betaMdsEllipse",
+      label = "Ellipses : ",
+      choices = c("..." = 0, sample_variables(physeq()))
+    )
+  )
+})
+
+output$betaMds <- metaRender2(renderPlot, {
+  validate(need(physeq(), "Requires an abundance dataset"),
+           need(length(input$betaMdsAxes) == 2, "Requires two projections axes"))
+  data <- physeq()
+  
+  betaMdsEllipse <- if (!is.null(checkNull(input$betaMdsEllipse))) {
+    metaExpr({
+      stat_ellipse(aes_string(group = ..(input$betaMdsEllipse)))
+    })
+  }
+  
+  metaExpr({
+    ord <- ordinate(data,
+                    method = ..(input$betaMdsMethod),
+                    distance = ..(input$betaDistance))
+    p <- plot_ordination(
+      physeq = data,
+      ordination = ord,
+      type = "samples",
+      axes = ..(as.numeric(input$betaMdsAxes)),
+      color = ..(checkNull(input$betaMdsCol)),
+      shape = ..(checkNull(input$betaMdsShape)),
+      label = ..(checkNull(input$betaMdsLabel)),
+      title = ..(checkNull(input$betaMdsTitle))
+    )
+    p <- p + ..(betaMdsEllipse)
+    p + theme_bw()
+  })
+})
+
+observeEvent(input$betaMds_output_code,
+             {
+               displayCodeModal(
+                 expandChain(
+                   quote(library(phyloseq)),
+                   quote(library(phyloseq.extended)),
+                   "# Replace `data` with you own data.",
+                   output$betaMds()
+                 )
+               )
+             }
+)
+
 output$betaClusterUI <- renderUI({
   validate(need(physeq(), ""))
   box(
@@ -13,7 +107,6 @@ output$betaClusterUI <- renderUI({
   )
 })
 
-
 output$betaCluster <- metaRender2(renderPlot, {
   validate(need(physeq(), "Requires an abundance dataset"))
   data <- physeq()

panels/richnessB-ui.R

+betaMds <- fluidPage(outputCodeButton(withLoader(plotOutput("betaMds", height = 700))),
+                     uiOutput("betaMdsUI"))
 betaCluster <- fluidPage(outputCodeButton(withLoader(plotOutput("betaCluster", height = 700))),
                         uiOutput("betaClusterUI"))
 betaHeatmap <- fluidPage(outputCodeButton(withLoader(plotOutput("betaHeatmap", height = 700))),

server.R

@@ -22,7 +22,6 @@ shinyServer
   source("panels/rarefactionCurve-server.R", local = TRUE)
   source("panels/richnessA-server.R", local = TRUE)
   source("panels/richnessB-server.R", local = TRUE)
-  source("panels/mds-server.R", local = TRUE)
   source("panels/pca-server.R", local = TRUE)
   source("panels/tree-server.R", local = TRUE)
 

ui.R

@@ -9,7 +9,6 @@ source("panels/heatmap-ui.R", local = TRUE)
 source("panels/rarefactionCurve-ui.R", local = TRUE)
 source("panels/richnessA-ui.R", local = TRUE)
 source("panels/richnessB-ui.R", local = TRUE)
-source("panels/mds-ui.R", local = TRUE)
 source("panels/pca-ui.R", local = TRUE)
 source("panels/tree-ui.R", local = TRUE)
 source("panels/Help-ui.R", local = TRUE)
@@ -68,12 +67,12 @@ dashboardHeader(title = "Easy16S"),
                selectInput("betaDistance",
                            label = "Distance : ",
                            choices = list("bray", "jaccard", "unifrac", "wunifrac", "dpcoa", "jsd", "euclidean")),
+               menuSubItem("MultiDimensional Scaling", tabName = "betaMds"),
                menuSubItem("Samples clustering", tabName = "betaCluster"),
                menuSubItem("Samples heatmap", tabName = "betaHeatmap"),
                menuSubItem("Network", tabName = "betaNetwork"),
                menuSubItem("Table", tabName = "betaTable")
       ),
-      menuItem("MultiDimensional Scaling", tabName = "mds", icon = icon("dot-circle")),
       menuItem("PCA", tabName = "pca", icon = icon("bullseye")),
       menuItem("Phylogenetic tree", tabName = "tree", icon = icon("tree")),
       menuItem("Help", tabName = "Help", icon = icon("info-circle"))
@@ -90,11 +89,11 @@ dashboardHeader(title = "Easy16S"),
       tabItem(tabName = "rarefactionCurve", rarefactionCurve),
       tabItem(tabName = "alphaPlot", alphaPlot),
       tabItem(tabName = "alphaTable", alphaTable),
+      tabItem(tabName = "betaMds", betaMds),
       tabItem(tabName = "betaCluster", betaCluster),
       tabItem(tabName = "betaHeatmap", betaHeatmap),
       tabItem(tabName = "betaNetwork", betaNetwork),
       tabItem(tabName = "betaTable", betaTable),
-      tabItem(tabName = "mds", mds),
       tabItem(tabName = "pca", pca),
       tabItem(tabName = "tree", tree),
       tabItem(tabName = "Help", Help)