Fixes plot settings that did not have an accordion wrapper (#1436)

averissimo · llrs-roche · web-flow · commit 040f0e073e01 · 2025-10-29T14:28:54.000+01:00
# Pull Request  - Fixes insightsengineering/teal.modules.general#937 Companion PR: - #1436 - insightsengineering/teal.modules.general#939 ### Note to reviewer :information_source: Please check each example app of the affected module ### Changes description - [x] Adds `bslib::accordion` wrapper to plot settings that were missing - [x] Check other modules / encoding if there are any that have the same problem --------- Co-authored-by: Lluís Revilla <185338939+llrs-roche@users.noreply.github.com>
diff --git a/R/tm_g_pp_adverse_events.R b/R/tm_g_pp_adverse_events.R
@@ -428,14 +428,16 @@ ui_g_adverse_events <- function(id, ...) {
         )
       ),
       ui_decorate_teal_data(ns("d_plot"), decorators = select_decorators(ui_args$decorators, "plot")),
-      bslib::accordion_panel(
-        title = "Plot settings",
+      bslib::accordion(
         open = TRUE,
-        teal.widgets::optionalSliderInputValMinMax(
-          ns("font_size"),
-          "Font Size",
-          ui_args$font_size,
-          ticks = FALSE, step = 1
+        bslib::accordion_panel(
+          title = "Plot settings",
+          teal.widgets::optionalSliderInputValMinMax(
+            ns("font_size"),
+            "Font Size",
+            ui_args$font_size,
+            ticks = FALSE, step = 1
+          )
         )
       )
     ),
@@ -631,7 +633,7 @@ srv_g_adverse_events <- function(id,
     output$table <- DT::renderDataTable(table_r()[["html"]])
 
     decorated_all_q <- reactive(
-# warning because of https://github.com/insightsengineering/teal.modules.clinical/issues/1427 # nolint: line_length_linter.
+      suppressWarnings(c(table_q(), decorated_all_q_plot())) # warning because of https://github.com/insightsengineering/teal.modules.clinical/issues/1427 # nolint: line_length_linter.
     )
 
     set_chunk_dims(pws, decorated_all_q)
diff --git a/R/tm_g_pp_patient_timeline.R b/R/tm_g_pp_patient_timeline.R
@@ -701,15 +701,17 @@ ui_g_patient_timeline <- function(id, ...) {
         )
       ),
       ui_decorate_teal_data(ns("decorator"), decorators = select_decorators(ui_args$decorators, "plot")),
-      bslib::accordion_panel(
-        title = "Plot settings",
+      bslib::accordion(
         open = TRUE,
-        teal.widgets::optionalSliderInputValMinMax(
-          ns("font_size"),
-          "Font Size",
-          ui_args$font_size,
-          ticks = FALSE,
-          step = 1
+        bslib::accordion_panel(
+          title = "Plot settings",
+          teal.widgets::optionalSliderInputValMinMax(
+            ns("font_size"),
+            "Font Size",
+            ui_args$font_size,
+            ticks = FALSE,
+            step = 1
+          )
         )
       )
     ),
diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R
@@ -530,15 +530,17 @@ ui_g_therapy <- function(id, ...) {
         is_single_dataset = is_single_dataset_value
       ),
       ui_decorate_teal_data(ns("d_plot"), decorators = select_decorators(ui_args$decorators, "plot")),
-      bslib::accordion_panel(
-        title = "Plot settings",
+      bslib::accordion(
         open = TRUE,
-        teal.widgets::optionalSliderInputValMinMax(
-          ns("font_size"),
-          "Font Size",
-          ui_args$font_size,
-          ticks = FALSE,
-          step = 1
+        bslib::accordion_panel(
+          title = "Plot settings",
+          teal.widgets::optionalSliderInputValMinMax(
+            ns("font_size"),
+            "Font Size",
+            ui_args$font_size,
+            ticks = FALSE,
+            step = 1
+          )
         )
       )
     ),
diff --git a/R/tm_g_pp_vitals.R b/R/tm_g_pp_vitals.R
@@ -394,12 +394,14 @@ ui_g_vitals <- function(id, ...) {
         is_single_dataset = is_single_dataset_value
       ),
       ui_decorate_teal_data(ns("decorator"), decorators = select_decorators(ui_args$decorators, "plot")),
-      bslib::accordion_panel(
-        title = "Plot settings",
+      bslib::accordion(
         open = TRUE,
-        teal.widgets::optionalSliderInputValMinMax(
-          ns("font_size"), "Font Size", ui_args$font_size,
-          ticks = FALSE, step = 1
+        bslib::accordion_panel(
+          title = "Plot settings",
+          teal.widgets::optionalSliderInputValMinMax(
+            ns("font_size"), "Font Size", ui_args$font_size,
+            ticks = FALSE, step = 1
+          )
         )
       )
     ),
diff --git a/R/tm_t_binary_outcome.R b/R/tm_t_binary_outcome.R
@@ -721,44 +721,46 @@ ui_t_binary_outcome <- function(id, ...) {
         checkboxInput(ns("add_total"), "Add All Patients column", value = a$add_total)
       ),
       ui_decorate_teal_data(ns("decorator"), decorators = select_decorators(a$decorators, "table")),
-      bslib::accordion_panel(
-        "Additional table settings",
+      bslib::accordion(
         open = TRUE,
-        teal.widgets::optionalSelectInput(
-          inputId = ns("prop_ci_method"),
-          label = "Method for Proportion CI",
-          choices = c(
-            "Wald, without correction" = "wald",
-            "Wald, with correction" = "waldcc",
-            "Clopper-Pearson" = "clopper-pearson",
-            "Wilson" = "wilson",
-            "Wilson, with correction" = "wilsonc",
-            "Jeffreys" = "jeffreys",
-            "Agresti-Coull" = "agresti-coull"
+        bslib::accordion_panel(
+          "Additional table settings",
+          teal.widgets::optionalSelectInput(
+            inputId = ns("prop_ci_method"),
+            label = "Method for Proportion CI",
+            choices = c(
+              "Wald, without correction" = "wald",
+              "Wald, with correction" = "waldcc",
+              "Clopper-Pearson" = "clopper-pearson",
+              "Wilson" = "wilson",
+              "Wilson, with correction" = "wilsonc",
+              "Jeffreys" = "jeffreys",
+              "Agresti-Coull" = "agresti-coull"
+            ),
+            selected = a$control$global$method,
+            multiple = FALSE,
+            fixed = FALSE
           ),
-          selected = a$control$global$method,
-          multiple = FALSE,
-          fixed = FALSE
-        ),
-        teal.widgets::optionalSelectInput(
-          inputId = ns("conf_level"),
-          label = "Confidence Level",
-          a$conf_level$choices,
-          a$conf_level$selected,
-          multiple = FALSE,
-          fixed = a$conf_level$fixed
+          teal.widgets::optionalSelectInput(
+            inputId = ns("conf_level"),
+            label = "Confidence Level",
+            a$conf_level$choices,
+            a$conf_level$selected,
+            multiple = FALSE,
+            fixed = a$conf_level$fixed
+          ),
+          bslib::input_switch(
+            id = ns("show_rsp_cat"),
+            label = "Show All Response Categories",
+            value = ifelse(a$rsp_table, TRUE, FALSE)
+          )
         ),
-        bslib::input_switch(
-          id = ns("show_rsp_cat"),
-          label = "Show All Response Categories",
-          value = ifelse(a$rsp_table, TRUE, FALSE)
+        teal.transform::data_extract_ui(
+          id = ns("aval_var"),
+          label = "Analysis Variable",
+          data_extract_spec = a$aval_var,
+          is_single_dataset = is_single_dataset_value
         )
-      ),
-      teal.transform::data_extract_ui(
-        id = ns("aval_var"),
-        label = "Analysis Variable",
-        data_extract_spec = a$aval_var,
-        is_single_dataset = is_single_dataset_value
       )
     ),
     pre_output = a$pre_output,
diff --git a/R/tm_t_events.R b/R/tm_t_events.R
@@ -636,42 +636,44 @@ ui_t_events_byterm <- function(id, ...) {
       ),
       checkboxInput(ns("add_total"), "Add All Patients columns", value = a$add_total),
       ui_decorate_teal_data(ns("decorator"), decorators = select_decorators(a$decorators, "table")),
-      bslib::accordion_panel(
-        "Additional table settings",
+      bslib::accordion(
         open = TRUE,
-        checkboxInput(
-          ns("drop_arm_levels"),
-          label = "Drop columns not in filtered analysis dataset",
-          value = a$drop_arm_levels
-        ),
-        selectInput(
-          inputId = ns("sort_criteria"),
-          label = "Sort Criteria",
-          choices = c(
-            "Decreasing frequency" = "freq_desc",
-            "Alphabetically" = "alpha"
+        bslib::accordion_panel(
+          "Additional table settings",
+          checkboxInput(
+            ns("drop_arm_levels"),
+            label = "Drop columns not in filtered analysis dataset",
+            value = a$drop_arm_levels
           ),
-          selected = a$sort_criteria,
-          multiple = FALSE
-        ),
-        helpText(tags$strong("Pruning Options:")),
-        numericInput(
-          inputId = ns("prune_freq"),
-          label = "Minimum Incidence Rate(%) in any of the treatment groups",
-          value = a$prune_freq,
-          min = 0,
-          max = 100,
-          step = 1,
-          width = "100%"
-        ),
-        numericInput(
-          inputId = ns("prune_diff"),
-          label = "Minimum Difference Rate(%) between any of the treatment groups",
-          value = a$prune_diff,
-          min = 0,
-          max = 100,
-          step = 1,
-          width = "100%"
+          selectInput(
+            inputId = ns("sort_criteria"),
+            label = "Sort Criteria",
+            choices = c(
+              "Decreasing frequency" = "freq_desc",
+              "Alphabetically" = "alpha"
+            ),
+            selected = a$sort_criteria,
+            multiple = FALSE
+          ),
+          helpText(tags$strong("Pruning Options:")),
+          numericInput(
+            inputId = ns("prune_freq"),
+            label = "Minimum Incidence Rate(%) in any of the treatment groups",
+            value = a$prune_freq,
+            min = 0,
+            max = 100,
+            step = 1,
+            width = "100%"
+          ),
+          numericInput(
+            inputId = ns("prune_diff"),
+            label = "Minimum Difference Rate(%) between any of the treatment groups",
+            value = a$prune_diff,
+            min = 0,
+            max = 100,
+            step = 1,
+            width = "100%"
+          )
         )
       )
     ),
diff --git a/R/tm_t_glm_counts.R b/R/tm_t_glm_counts.R
@@ -211,17 +211,21 @@ ui_t_glm_counts <- function(id, ...) {
     )
   )
 
-  table_settings <- bslib::accordion_panel(
-    "Additional table settings",
-    teal.widgets::optionalSelectInput(
-      inputId = ns("conf_level"),
-      label = "Confidence Level",
-      choices = c(0.8, 0.9, 0.95),
-      selected = 0.95,
-      multiple = FALSE,
-      fixed = FALSE
-    ),
+  table_settings <- shiny::tagList(
     ui_decorate_teal_data(ns("decorator"), decorators = select_decorators(a$decorators, "table")),
+    bslib::accordion(
+      bslib::accordion_panel(
+        "Additional table settings",
+        teal.widgets::optionalSelectInput(
+          inputId = ns("conf_level"),
+          label = "Confidence Level",
+          choices = c(0.8, 0.9, 0.95),
+          selected = 0.95,
+          multiple = FALSE,
+          fixed = FALSE
+        ),
+      )
+    )
   )
 
   teal.widgets::standard_layout(
@@ -269,7 +273,7 @@ ui_t_glm_counts <- function(id, ...) {
         "Rate method",
         choices = a$rate_mean_method
       ),
-      table_settings,
+      table_settings
     ),
     pre_output = a$pre_output,
     post_output = a$post_output
diff --git a/R/tm_t_tte.R b/R/tm_t_tte.R
