Follow changes in nexus

tesselle · Apr 9, 2024 · f2df7bd · f2df7bd
1 parent a11b8af
commit f2df7bd
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Showing 2 changed files with 41 additions and 69 deletions.
diff --git a/R/module_coda.R b/R/module_coda.R
@@ -10,49 +10,47 @@ coda_ui <- function(id) {
   # Create a namespace function using the provided id
   ns <- NS(id)
 
-  fluidRow(
-    column(
-      width = 4,
-      wellPanel(
-        selectizeInput(
-          inputId = ns("codes"),
-          label = bslib::tooltip(
-            span("Unique identifiers", icon("info-circle")),
-            "Define the unique identifier (eg. laboratory codes) of each observation."
-          ),
-          choices = NULL,
-          selected = NULL,
-          multiple = FALSE,
-          options = list(plugins = "clear_button")
+  sidebarLayout(
+    sidebarPanel(
+      selectizeInput(
+        inputId = ns("codes"),
+        label = bslib::tooltip(
+          span("Unique identifiers", icon("info-circle")),
+          "Define the unique identifier (eg. laboratory codes) of each observation."
         ),
-        selectizeInput(
-          inputId = ns("samples"),
-          label = bslib::tooltip(
-            span("Sample names", icon("info-circle")),
-            "Duplicated sample names will be interpreted as repeated measurements."
-          ),
-          choices = NULL,
-          selected = NULL,
-          multiple = FALSE,
-          options = list(plugins = "clear_button")
+        choices = NULL,
+        selected = NULL,
+        multiple = FALSE,
+        options = list(plugins = "clear_button")
+      ),
+      selectizeInput(
+        inputId = ns("samples"),
+        label = bslib::tooltip(
+          span("Sample names", icon("info-circle")),
+          "Duplicated sample names will be interpreted as repeated measurements."
         ),
-        selectizeInput(
-          inputId = ns("groups"),
-          label = bslib::tooltip(
-            span("Groups", icon("info-circle")),
-            "Empty strings will be interpreted as unassigned samples."
-          ),
-          choices = NULL,
-          selected = NULL,
-          multiple = FALSE,
-          options = list(plugins = "clear_button")
-        )
-      ), # wellPanel
+        choices = NULL,
+        selected = NULL,
+        multiple = FALSE,
+        options = list(plugins = "clear_button")
+      ),
+      selectizeInput(
+        inputId = ns("groups"),
+        label = bslib::tooltip(
+          span("Groups", icon("info-circle")),
+          "Empty strings will be interpreted as unassigned samples."
+        ),
+        choices = NULL,
+        selected = NULL,
+        multiple = FALSE,
+        options = list(plugins = "clear_button")
+      ),
+      hr(),
       ## Output: display description
+      h5("Description"),
       uiOutput(outputId = ns("description"))
-    ), # column
-    column(
-      width = 8,
+    ), # sidebarPanel
+    mainPanel(
       tabsetPanel(
         tabPanel(
           title = "Detection limits",
@@ -72,8 +70,8 @@ coda_ui <- function(id) {
           DT::dataTableOutput(outputId = ns("table"))
         )
       )
-    ) # column
-  ) # fluidRow
+    ) # mainPanel
+  ) # sidebarLayout
 }
 
 # Server =======================================================================
@@ -213,33 +211,8 @@ coda_server <- function(id, x) {
 
     output$description <- renderUI({
       req(clean())
-      assigned <- nexus::is_assigned(clean())
-      n_col <- ncol(clean())
-      n_obs <- nrow(clean())
-      n_spl <- length(unique(nexus::get_samples(clean())))
-      n_rep <- sum(nexus::is_replicated(clean()))
-      n_grp <- length(unique(nexus::get_groups(clean())[assigned]))
-      n_out <- sum(!assigned)
-
-      msg_parts <- sprintf("%d parts: %s", n_col, paste0(colnames(clean()), collapse = ", "))
-      msg_obs <- sprintf("%d %s:", n_obs, ngettext(n_obs, "observation", "observations"))
-      msg_spl <- sprintf("%d unique %s", n_spl, ngettext(n_spl, "sample", "samples"))
-      msg_rep <- sprintf("%d replicated %s", n_rep, ngettext(n_rep, "observation", "observations"))
-      msg_grp <- sprintf("%d %s", n_grp, ngettext(n_grp, "group", "groups"))
-      msg_out <- sprintf("%d unassigned %s", n_out, ngettext(n_out, "sample", "samples"))
-
-      tags$ul(
-        class = "list-group list-group-flush",
-        tags$li(class="list-group-item", msg_parts),
-        tags$li(class="list-group-item", msg_spl),
-        tags$li(class="list-group-item", msg_rep),
-        tags$li(
-          class="list-group-item",
-          msg_grp,
-          tags$ul(class = "list-group list-group-flush", list_group())
-        ),
-        tags$li(class="list-group-item", msg_out)
-      )
+      descr <- capture.output(nexus::describe(clean()))
+      markdown(descr)
     })
 
     ## Render tables -----

diff --git a/R/module_data.R b/R/module_data.R
@@ -386,7 +386,6 @@ prepare_server <- function(id, x) {
         x = data_clean(),
         val = input
       )
-      print(each_var)
       keep <- Reduce(f = `&`, x = each_var)
       if (all(!keep)) return(data_clean())
       data_clean()[keep, , drop = FALSE]