Add pairwise compairison in alpha-diversity ANOVA

panels/richnessA-server.R

@@ -136,7 +136,7 @@ output$alphaAnovaUI <- renderUI({
   )
 })
 
-output$alphaAnova <- renderPrint({
+model <- reactive({
   validate(
     need(physeq(), "Requires an abundance dataset"),
     need(input$anovaRichnessMeasure, ""),
@@ -145,8 +145,28 @@ output$alphaAnova <- renderPrint({
   anova_data <- cbind(estimate_richness(physeq(), measures = input$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)
+  do.call("lm", list(formula = as.formula(formula), data = as.name("anova_data")))
+})
+
+output$alphaAnova <- renderPrint({
+  validate(need(model(), ""))
+  print(model())
+  anova(model())
 })
 
+output$anovaHSD <- DT::renderDT({
+  validate(
+    need(model(), ""),
+    need(physeq(), "Requires an abundance dataset"),
+    need(input$anovaRichnessMeasure, ""),
+    need(input$anovaCovariate, "Select a covariate")
+  )
+  var <- get_variable(physeq(), input$anovaCovariate)
+  if (! (is.factor(var) || is.character(var))) {
+    tibble::tibble(.rows = 0)
+  } else {
+    TukeyHSD(aov(model()))[[1]] %>% as_tibble(rownames = "Pair") %>%
+      beautifulTable() %>%
+      DT::formatSignif(columns = c("diff", "lwr", "upr", "p adj"), digits = 4)
+  }
+})

panels/richnessA-ui.R

@@ -2,5 +2,12 @@ alphaPlot <- fluidPage(outputCodeButton(withLoader(plotOutput("alphaPlot", heigh
                        uiOutput("alphaPlotUI"))
 alphaTable <- fluidPage(uiOutput("alphaTable"))
 alphaAnova <- fluidPage(uiOutput("alphaAnovaUI"),
-                        verbatimTextOutput("alphaAnova")
+                        verbatimTextOutput("alphaAnova"),
+                        box(
+                          title = "Table of pairwise comparisons",
+                          width = NULL,
+                          status = "primary",
+                          collapsible = TRUE,
+                          collapsed = TRUE,
+                          DT::DTOutput("anovaHSD"))
                         )