Add anova module for alpha diversity

panels/richnessA-server.R

@@ -62,15 +62,15 @@ output$alphaPlotUI <- renderUI({
 output$alphaPlot <- metaRender2(renderPlot, {
   validate(need(physeq(), "Requires an abundance dataset"))
   data <- physeq()
-  
+
   alphaPlot_boxplot <- if (input$richnessBoxplot >= 2) {
     metaExpr({geom_boxplot()})
   }
-  
+
   alphaPlot_point <- if (input$richnessBoxplot <= 2) {
     metaExpr({geom_point()})
   }
-  
+
   metaExpr({
     p <- plot_richness(
       physeq = data,
@@ -106,3 +106,47 @@ output$alphaTable <- renderUI({
     beautifulTable(tibble::rownames_to_column(round(estimate_richness(physeq()), digits = 2), var = "SAMPLE"))
   )
 })
+
+output$alphaAnovaUI <- renderUI({
+  validate(need(physeq(), "Requires an abundance dataset"))
+  box(
+    title = "Alpha diversity Anova analysis",
+    width = NULL,
+    status = "primary",
+    selectInput(
+      inputId = "anovaRichnessMeasure",
+      label = "Richness measure : ",
+      choices = c(
+        "Observed",
+        "Chao1",
+        "ACE",
+        "Shannon",
+        "Simpson",
+        "InvSimpson",
+        "Fisher"
+      ),
+      selected = "Observed",
+      multiple = FALSE
+    ),
+    selectInput(
+      inputId = "anovaCovariate",
+      label = "Covariate : ",
+      choices = c(sample_variables(physeq()))
+    )
+  )
+})
+
+output$alphaAnova <- renderPrint({
+  validate(
+    need(physeq(), "Requires an abundance dataset"),
+    need(input$anovaRichnessMeasure, ""),
+    need(input$anovaCovariate, "Select a covariate")
+  )
+  anova_data <- cbind(estimate_richness(physeq(), measures = input$anovaRichnessMeasure),
+                      as(sample_data(physeq()), "data.frame"))
+  formula <-  paste0(input$anovaRichnessMeasure, " ~ ", input$anovaCovariate)
+  model <- do.call("lm", list(formula = as.formula(formula), data = as.name("anova_data")))
+  print(model)
+  anova(model)
+})
+

panels/richnessA-ui.R

 alphaPlot <- fluidPage(outputCodeButton(withLoader(plotOutput("alphaPlot", height = 700))),
                        uiOutput("alphaPlotUI"))
 alphaTable <- fluidPage(uiOutput("alphaTable"))
+alphaAnova <- fluidPage(uiOutput("alphaAnovaUI"),
+                        verbatimTextOutput("alphaAnova")
+                        )

ui.R

@@ -17,18 +17,18 @@ source("panels/Help-ui.R", local = TRUE)
 shinyUI(dashboardPage(
 dashboardHeader(title = "Easy16S"),
   dashboardSidebar(
-    actionButton("dataButton", 
-                 "Select your data", 
+    actionButton("dataButton",
+                 "Select your data",
                  icon = icon("upload"),
                  width = 200
                  ),
-    actionButton("filterButton", 
+    actionButton("filterButton",
                  "Select some samples",
                  icon = icon("filter"),
                  width = 200
                  ),
-    actionButton("transformButton", 
-                 "Transform abundance", 
+    actionButton("transformButton",
+                 "Transform abundance",
                  icon = icon("square-root-alt"),
                  width = 200
                  ),
@@ -39,13 +39,13 @@ dashboardHeader(title = "Easy16S"),
                               size = "mini",
                               width = 200
                               ),
-    actionButton("downloadButton", 
-                 "Download data", 
+    actionButton("downloadButton",
+                 "Download data",
                  icon = icon("download"),
                  width = 200
                  ),
-    actionButton("plotButton", 
-                 "Download last plot", 
+    actionButton("plotButton",
+                 "Download last plot",
                  icon = icon("file-image"),
                  width = 200
                  ),
@@ -62,7 +62,8 @@ dashboardHeader(title = "Easy16S"),
       menuItem("Rarefaction curves", tabName = "rarefactionCurve", icon = icon("chart-line")),
       menuItem(HTML("α-diversity"), icon = icon("th"),
                menuSubItem("Plots", tabName = "alphaPlot"),
-               menuSubItem("Table", tabName = "alphaTable")
+               menuSubItem("Table", tabName = "alphaTable"),
+               menuSubItem("ANOVA", tabName = "alphaAnova")
       ),
       menuItem(HTML("β-diversity"), icon = icon("th"),
                selectInput("betaDistance",
@@ -92,6 +93,7 @@ dashboardHeader(title = "Easy16S"),
       tabItem(tabName = "rarefactionCurve", rarefactionCurve),
       tabItem(tabName = "alphaPlot", alphaPlot),
       tabItem(tabName = "alphaTable", alphaTable),
+      tabItem(tabName = "alphaAnova", alphaAnova),
       tabItem(tabName = "betaMds", betaMds),
       tabItem(tabName = "betaCluster", betaCluster),
       tabItem(tabName = "betaManova", betaManova),