adonis

panels/richnessB-server.R

@@ -5,6 +5,7 @@ betaDist <- metaReactive2({
     })
   })
 
+## MDS
 output$betaMdsUI <- renderUI({
   validate(need(physeq(), ""))
   box(
@@ -100,6 +101,7 @@ observeEvent(input$betaMds_output_code,
              }
 )
 
+## Cluster
 output$betaClusterUI <- renderUI({
   validate(need(physeq(), ""))
   box(
@@ -142,6 +144,34 @@ observeEvent(input$betaCluster_output_code,
              }
 )
 
+## MANOVA
+output$betaManovaUI <- renderUI({
+  validate(need(physeq(), ""))
+  box(
+    title = "Setting : " ,
+    width = NULL,
+    status = "primary",
+    selectInput("betaManovaVar",
+                label = "Covariates",
+                multiple = TRUE,
+                choices = c(sample_variables(physeq())),
+                selected = NULL)#,
+    # actionButton("betaManovaButton",
+    #              "Compute"),
+  )
+})
+
+output$betaManova <- renderPrint({
+  validate(need(physeq(), "Requires an abundance dataset"))
+  validate(need(input$betaManovaVar, "Requires at least one covariate"))
+
+  vegan::adonis(
+    as.formula(paste("betaDist()", "~", paste(input$betaManovaVar, collapse = "*"))),
+    data = as(sample_data(physeq()), "data.frame"),
+    perm = 9999)
+})
+
+## Heatmap
 output$betaHeatmapUI <- renderUI({
   validate(need(physeq(), ""))
   box(
@@ -211,6 +241,7 @@ observeEvent(input$betaHeatmap_output_code,
              }
 )
 
+## Network
 output$betaNetworkUI <- renderUI({
   validate(need(physeq(), ""))
   box(
@@ -275,6 +306,7 @@ observeEvent(input$betaNetwork_output_code,
              }
 )
 
+## Table
 output$betaTable <- renderUI({
   validate(need(physeq(), "Requires an abundance dataset"))
   box(

panels/richnessB-ui.R

@@ -2,8 +2,11 @@ betaMds <- fluidPage(outputCodeButton(withLoader(plotOutput("betaMds", height =
                      uiOutput("betaMdsUI"))
 betaCluster <- fluidPage(outputCodeButton(withLoader(plotOutput("betaCluster", height = 700))),
                         uiOutput("betaClusterUI"))
-betaHeatmap <- fluidPage(outputCodeButton(withLoader(plotOutput("betaHeatmap", height = 700))),
-                         uiOutput("betaHeatmapUI"))
+betaManova <- fluidPage(withLoader(verbatimTextOutput("betaManova")),
+                           uiOutput("betaManovaUI"),
+                           verbatimTextOutput("betaManova2"))
 betaNetwork <- fluidPage(outputCodeButton(withLoader(plotOutput("betaNetwork", height = 700))),
                           uiOutput("betaNetworkUI"))
+betaHeatmap <- fluidPage(outputCodeButton(withLoader(plotOutput("betaHeatmap", height = 700))),
+                         uiOutput("betaHeatmapUI"))
 betaTable <- fluidPage(uiOutput("betaTable"))

ui.R

@@ -69,6 +69,7 @@ dashboardHeader(title = "Easy16S"),
                            choices = list("bray", "jaccard", "unifrac", "wunifrac", "dpcoa", "jsd", "euclidean")),
                menuSubItem("MultiDimensional Scaling", tabName = "betaMds"),
                menuSubItem("Samples clustering", tabName = "betaCluster"),
+               menuSubItem("Multivariate ANOVA", tabName = "betaManova"),
                menuSubItem("Network", tabName = "betaNetwork"),
                menuSubItem("Samples heatmap", tabName = "betaHeatmap"),
                menuSubItem("Table", tabName = "betaTable")
@@ -91,6 +92,7 @@ dashboardHeader(title = "Easy16S"),
       tabItem(tabName = "alphaTable", alphaTable),
       tabItem(tabName = "betaMds", betaMds),
       tabItem(tabName = "betaCluster", betaCluster),
+      tabItem(tabName = "betaManova", betaManova),
       tabItem(tabName = "betaNetwork", betaNetwork),
       tabItem(tabName = "betaHeatmap", betaHeatmap),
       tabItem(tabName = "betaTable", betaTable),