From 961d78a644a723f0eb004cae762f39051a85b762 Mon Sep 17 00:00:00 2001
From: nfrerebeau <nicolas.frerebeau@u-bordeaux-montaigne.fr>
Date: Tue, 22 Oct 2024 19:20:30 +0200
Subject: [PATCH] Follow changes in nexus

---
 R/coda_plot.R       | 66 ++++++++++++++++++++++++---------------------
 R/coda_statistics.R | 40 +++++++--------------------
 2 files changed, 46 insertions(+), 60 deletions(-)

diff --git a/R/coda_plot.R b/R/coda_plot.R
index 2bea40c..b55e83b 100644
--- a/R/coda_plot.R
+++ b/R/coda_plot.R
@@ -13,24 +13,6 @@ coda_plot_ui <- function(id) {
   layout_sidebar(
     sidebar = sidebar(
       width = 400,
-      checkboxInput(
-        inputId = ns("order_columns"),
-        label = "Sort columns",
-        value = FALSE
-      ),
-      selectInput(
-        inputId = ns("order_rows"),
-        label = "Row order",
-        choices = NULL,
-        selected = NULL,
-        multiple = FALSE,
-      ),
-      checkboxInput(
-        inputId = ns("decreasing"),
-        label = "Decreasing row order",
-        value = FALSE
-      ),
-      hr(),
       checkboxInput(
         inputId = ns("select_major"),
         label = "Major elements",
@@ -46,6 +28,23 @@ coda_plot_ui <- function(id) {
         label = "Trace elements",
         value = TRUE
       ),
+      hr(),
+      checkboxInput(
+        inputId = ns("order_columns"),
+        label = "Sort columns",
+        value = FALSE
+      ),
+      selectizeInput(
+        inputId = ns("order_rows"),
+        label = "Row order",
+        choices = NULL, selected = NULL, multiple = FALSE,
+        options = list(plugins = "remove_button")
+      ),
+      checkboxInput(
+        inputId = ns("decreasing"),
+        label = "Decreasing row order",
+        value = FALSE
+      )
     ), # sidebar
     output_plot(
       id = ns("plot"),
@@ -73,19 +72,18 @@ coda_plot_server <- function(id, x) {
   stopifnot(is.reactive(x))
 
   moduleServer(id, function(input, output, session) {
-    ## Build barplot -----
     bindEvent(
       observe({
         freezeReactiveValue(input, "order_rows")
-        choices <- c("", colnames(x()))
-        updateSelectInput(inputId = "order_rows", choices = choices)
+        choices <- c("", colnames(data_bar()))
+        updateSelectizeInput(inputId = "order_rows", choices = choices)
       }),
-      x()
+      data_bar()
     )
-    plot_bar <- reactive({
-      req(x())
 
-      col <- khroma::color(input$color_qualitative)
+    ## Subset -----
+    data_bar <- reactive({
+      req(x())
 
       elements <- logical(ncol(x()))
       is_major <- nexus::is_element_major(x())
@@ -96,15 +94,23 @@ coda_plot_server <- function(id, x) {
       elements[which(is_minor)] <- input$select_minor
       elements[which(is_trace)] <- input$select_trace
 
-      if (!any(elements)) elements <- NULL
+      if (!any(elements)) return(x())
+      x()[, elements, drop = FALSE]
+    })
+
+    ## Build barplot -----
+    plot_bar <- reactive({
+      req(data_bar())
+
+      col <- khroma::color(input$color_qualitative)
+      pal <- khroma::palette_color_discrete(col, domain = colnames(x()))
 
       nexus::barplot(
-        height = x(),
-        select = elements,
+        height = data_bar(),
         order_columns = input$order_columns,
-        order_rows = input$order_rows,
+        order_rows = get_value(input$order_rows),
         decreasing = input$decreasing,
-        color = khroma::palette_color_discrete(col)
+        color = pal
       )
       grDevices::recordPlot()
     })
diff --git a/R/coda_statistics.R b/R/coda_statistics.R
index 6d85418..aaeda54 100644
--- a/R/coda_statistics.R
+++ b/R/coda_statistics.R
@@ -39,11 +39,6 @@ coda_summary_ui <- function(id) {
         gt::gt_output(outputId = ns("mean")),
         gt::gt_output(outputId = ns("quantile"))
       ),
-      # nav_panel(
-      #   title = "Spread",
-      #   helpText(info_article("Hron & Kubacek", "2011", "10.1007/s00184-010-0299-3")),
-      #   gt::gt_output(outputId = ns("spread")),
-      # ),
       nav_panel(
         title = "Covariance",
         gt::gt_output(outputId = ns("covariance"))
@@ -79,11 +74,6 @@ coda_summary_server <- function(id, x) {
   stopifnot(is.reactive(x))
 
   moduleServer(id, function(input, output, session) {
-    ## Validate -----
-    data <- reactive({
-      x()
-    })
-
     ## Location -----
     data_loc <- reactive({
       req(x())
@@ -97,19 +87,7 @@ coda_summary_server <- function(id, x) {
     })
 
     ## Spread -----
-    data_spread <- reactive({
-      req(x())
-      ## Metric variance by group
-      if (nexus::any_assigned(x())) {
-        index <- nexus::groups(x())
-        s <- nexus::aggregate(x(), by = index, FUN = nexus::variance_total)
-      } else {
-        m <- nexus::variance_total(x())
-        s <- matrix(m, nrow = 1, dimnames = list("", NULL))
-      }
-      colnames(s) <- c("metric variance")
-      s
-    })
+    # TODO
 
     ## Percentiles -----
     data_quant <- reactive({
@@ -118,14 +96,17 @@ coda_summary_server <- function(id, x) {
     })
 
     ## Histogram -----
-    observeEvent(x(), {
-      choices <- colnames(x())
-      freezeReactiveValue(input, "hist_select")
-      updateSelectInput(inputId = "hist_select", choices = choices)
-    })
+    bindEvent(
+      observe({
+        choices <- colnames(x())
+        freezeReactiveValue(input, "hist_select")
+        updateSelectInput(inputId = "hist_select", choices = choices)
+      }),
+      x()
+    )
     plot_hist <- reactive({
       req(x())
-      nexus::hist(x()[, input$hist_select, drop = FALSE], ncol = 1)
+      nexus::hist(x(), select = input$hist_select)
       grDevices::recordPlot()
     })
 
@@ -238,7 +219,6 @@ coda_summary_server <- function(id, x) {
     ## Download -----
     output$download <- export_multiple(
       location = data_loc,
-      # spread = data_spread,
       quantiles = data_quant,
       covariance = data_cov,
       variation = data_var,