Display only compositional statistics

tesselle · Dec 15, 2023 · 50ac956 · 50ac956
1 parent 38ebdcd
commit 50ac956
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Showing 4 changed files with 56 additions and 40 deletions.
diff --git a/R/module_coda.R b/R/module_coda.R
@@ -14,12 +14,14 @@ module_coda_ui <- function(id) {
     column(
       width = 4,
       wellPanel(
+        helpText("Define the unique identifier (eg. laboratory codes) of each observation."),
         selectizeInput(
           inputId = ns("codes"),
           label = "Unique identifiers",
           choices = NULL,
           selected = NULL,
           multiple = FALSE,
+          options = list(plugins = "clear_button")
         ),
         helpText("Duplicated sample names will be interpreted as repeated measurements."),
         selectizeInput(
@@ -28,6 +30,7 @@ module_coda_ui <- function(id) {
           choices = NULL,
           selected = NULL,
           multiple = FALSE,
+          options = list(plugins = "clear_button")
         ),
         helpText("Empty strings can be used to specify that a sample does not belong to any group."),
         selectizeInput(
@@ -36,6 +39,7 @@ module_coda_ui <- function(id) {
           choices = NULL,
           selected = NULL,
           multiple = FALSE,
+          options = list(plugins = "clear_button")
         )
       ), # wellPanel
       ## Output: display description

diff --git a/R/module_coda_summary.R b/R/module_coda_summary.R
@@ -10,40 +10,42 @@ module_coda_summary_ui <- function(id) {
   ## Create a namespace function using the provided id
   ns <- NS(id)
 
-  sidebarLayout(
-    sidebarPanel(
-      downloadButton(outputId = ns("download"), "Download")
-    ), # sidebarPanel
-    mainPanel(
+  fluidRow(
+    column(
+      width = 4,
+      wellPanel(
+        style = "margin-bottom: 15px;",
+        h5("Compositional statistics"),
+        downloadButton(outputId = ns("download"), "Download tables")
+      ), # wellPanel
+      output_plot(id = ns("dendrogram"), height = "auto", title = "Variation matrix")
+    ), # column
+    column(
+      width = 8,
       tabsetPanel(
         type = "tabs",
         tabPanel(
           title = "Summary statistics",
           h5("Center"),
-          tableOutput(outputId = ns("location"))
+          tableOutput(outputId = ns("location")),
+          h5("Percentile table"),
+          tableOutput(outputId = ns("quantile"))
+        ),
+        tabPanel(
+          title = "Univariate statistics",
+          output_plot(id = ns("hist"), height = "auto", title = "Histogram")
         ),
         tabPanel(
           title = "CLR covariance",
           tableOutput(outputId = ns("covariance"))
         ),
         tabPanel(
           title = "Variation matrix",
-          fluidRow(
-            div(
-              class = "col-lg-6 col-md-1",
-              output_plot(id = ns("dendrogram"), height = "auto", title = "Heatmap")
-            ),
-            div(
-              class = "col-lg-6 col-md-1"
-            )
-          ),
-          fluidRow(
-            tableOutput(outputId = ns("variation"))
-          )
+          tableOutput(outputId = ns("variation"))
         )
       ) # tabsetPanel
-    ) # mainPanel
-  ) # sidebarLayout
+    ) # column
+  ) # fluidRow
 }
 
 # Server =======================================================================
@@ -60,55 +62,73 @@ module_coda_summary_server <- function(id, x) {
   stopifnot(is.reactive(x))
 
   moduleServer(id, function(input, output, session) {
-    ## Location
+    ## Location -----
     data_loc <- reactive({
       req(x())
       if (nexus::any_assigned(x())) {
-        nexus::aggregate(x(), by = "groups", FUN = mean, na.rm = FALSE)
+        index <- nexus::get_groups(x())
+        nexus::aggregate(x(), by = index, FUN = nexus::mean, na.rm = FALSE)
       } else {
-        moy <- colMeans(x(), na.rm = FALSE)
-        matrix(moy, ncol = length(moy), dimnames = list("", names(moy)))
+        m <- nexus::mean(x(), na.rm = FALSE)
+        matrix(m, nrow = 1, dimnames = list("center", names(m)))
       }
     })
 
-    ## CLR covariance
+    ## Percentiles -----
+    data_quant <- reactive({
+      req(x())
+      nexus::quantile(x(), probs = seq(0, 1, 0.25))
+    })
+
+    ## Histograms -----
+    plot_hist <- reactive({
+      req(x())
+      nexus::hist(x()[, 1:6, drop = FALSE], ncol = 3)
+      grDevices::recordPlot()
+    })
+
+    ## CLR covariance -----
     data_cov <- reactive({
       req(x())
       nexus::covariance(x(), center = TRUE)
     })
 
-    ## Variation matrix
+    ## Variation matrix -----
     data_var <- reactive({
       req(x())
       nexus::variation(x())
     })
 
-    ## Clustering
+    ## Clustering -----
     # plot_clust <- reactive({
     #   d <- stats::as.dist(data_var())
     #   h <- stats::hclust(d, method = "ward.D2")
     #   plot(h, main = "", sub = "", xlab = "", ylab = "Total variation", las = 1)
     #   grDevices::recordPlot()
     # })
 
+    ## Heatmap -----
     plot_heatmap <- reactive({
       stats::heatmap(data_var(), distfun = stats::as.dist,
                      hclustfun = function(x) stats::hclust(x, method = "ward.D2"),
                      symm = TRUE, scale = "none")
       grDevices::recordPlot()
     })
 
-    ## Render table
+    ## Render table -----
     output$location <- renderTable({data_loc()}, striped = TRUE, width = "100%", rownames = TRUE)
+    output$quantile <- renderTable({data_quant()}, striped = TRUE, width = "100%", rownames = TRUE)
     output$covariance <- renderTable({data_cov()}, striped = TRUE, width = "100%", rownames = TRUE)
     output$variation <- renderTable({data_var()}, striped = TRUE, width = "100%", rownames = TRUE)
 
-    ## Render plot
+    ## Render plot -----
     render_plot("dendrogram", x = plot_heatmap)
+    render_plot("hist", x = plot_hist, height = function() { getCurrentOutputInfo(session)$width() / 2 })
 
-    ## Download
+    ## Download -----
     output$download <- export_table(
       location = data_loc,
+      quantiles = data_quant,
       covariance = data_cov,
       variation = data_var,
       name = "coda_summary"

diff --git a/inst/coda/server.R b/inst/coda/server.R
@@ -15,7 +15,6 @@ shiny_server <- function(input, output, session) {
   coda <- janus::module_coda_server("coda", x = clean)
 
   ## Statistics
-  janus::module_summary_server("summary", coda)
   janus::module_coda_summary_server("coda_summary", coda)
 
   ## Graphs

diff --git a/inst/coda/ui.R b/inst/coda/ui.R
@@ -34,16 +34,9 @@ shiny_ui <- function(request) {
           ) # tabPanel
         ) # tabsetPanel
       ), # tabPanel
-      navbarMenu(
+      tabPanel(
         title = "Statistics",
-        tabPanel(
-          title = "Classical statistics",
-          janus::module_summary_ui("summary")
-        ), # tabPanel
-        tabPanel(
-          title = "Compositional statistics",
-          janus::module_coda_summary_ui("coda_summary")
-        ) # tabPanel
+        janus::module_coda_summary_ui("coda_summary")
       ), # tabPanel
       navbarMenu(
         title = "Graph",