Follow changes in nexus

tesselle · Oct 17, 2024 · 1f7cf19 · 1f7cf19
1 parent 0b86f90
commit 1f7cf19
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Showing 4 changed files with 35 additions and 7 deletions.
diff --git a/R/coda.R b/R/coda.R
@@ -190,7 +190,7 @@ coda_server <- function(id, x) {
       req(clean())
       if (nexus::any_assigned(clean())) {
         tbl <- data.frame(group = nexus::groups(clean()), clean())
-        gt <- gt::gt(tbl, groupname_col="group", rownames_to_stub = TRUE)
+        gt <- gt::gt(tbl, groupname_col = "group", rownames_to_stub = TRUE)
       } else {
         gt <- clean() |>
           as.data.frame() |>

diff --git a/R/coda_outliers.R b/R/coda_outliers.R
@@ -78,9 +78,8 @@ coda_outliers_server <- function(id, x) {
 
         run_with_notification(
           {
-            nexus::outliers(
+            nexus::detect_outlier(
               x(),
-              groups = nexus::groups(x()),
               method = input$method,
               quantile = input$quantile
             )

diff --git a/R/coda_plot.R b/R/coda_plot.R
@@ -29,7 +29,23 @@ coda_plot_ui <- function(id) {
         inputId = ns("decreasing"),
         label = "Decreasing row order",
         value = FALSE
-      )
+      ),
+      hr(),
+      checkboxInput(
+        inputId = ns("select_major"),
+        label = "Major elements",
+        value = TRUE
+      ),
+      checkboxInput(
+        inputId = ns("select_minor"),
+        label = "Minor elements",
+        value = TRUE
+      ),
+      checkboxInput(
+        inputId = ns("select_trace"),
+        label = "Trace elements",
+        value = TRUE
+      ),
     ), # sidebar
     output_plot(
       id = ns("plot"),
@@ -70,8 +86,21 @@ coda_plot_server <- function(id, x) {
       req(x())
 
       col <- khroma::color(input$color_qualitative)
+
+      elements <- logical(ncol(x()))
+      is_major <- nexus::is_element_major(x())
+      is_minor <- nexus::is_element_minor(x())
+      is_trace <- nexus::is_element_trace(x())
+
+      elements[which(is_major)] <- input$select_major
+      elements[which(is_minor)] <- input$select_minor
+      elements[which(is_trace)] <- input$select_trace
+
+      if (!any(elements)) elements <- NULL
+
       nexus::barplot(
         height = x(),
+        select = elements,
         order_columns = input$order_columns,
         order_rows = input$order_rows,
         decreasing = input$decreasing,

diff --git a/R/coda_statistics.R b/R/coda_statistics.R
@@ -98,9 +98,9 @@ coda_summary_server <- function(id, x) {
       ## Metric variance by group
       if (nexus::any_assigned(x())) {
         index <- nexus::groups(x())
-        s <- nexus::aggregate(x(), by = index, FUN = nexus::metric_var)
+        s <- nexus::aggregate(x(), by = index, FUN = nexus::variance_total)
       } else {
-        m <- nexus::metric_var(x())
+        m <- nexus::variance_total(x())
         s <- matrix(m, nrow = 1, dimnames = list("", NULL))
       }
       colnames(s) <- c("metric variance")
@@ -234,7 +234,7 @@ coda_summary_server <- function(id, x) {
     ## Download -----
     output$download <- export_multiple(
       location = data_loc,
-      spread = data_spread,
+      # spread = data_spread,
       quantiles = data_quant,
       covariance = data_cov,
       variation = data_var,