Adds decorators to tm_t_smq (#1292)

Part of insightsengineering/teal#1371

<details>
<summary>Working example</summary>

```r
pkgload::load_all("../teal.modules.clinical", export_all = FALSE)
# Example below

insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") {
  teal_transform_module(
    label = "New row",
    ui = function(id) shiny::textInput(shiny::NS(id, "new_row"), "New row", value = default_caption),
    server = make_teal_transform_server(
      substitute({
        .var_to_replace <- rtables::insert_rrow(.var_to_replace, rtables::rrow(new_row))
      }, env = list(.var_to_replace = as.name(.var_to_replace)))
    )
  )
}

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADAE <- tmc_ex_adae

  .names_baskets <- grep("^(SMQ|CQ).*NAM$", names(ADAE), value = TRUE)
  .names_scopes <- grep("^SMQ.*SC$", names(ADAE), value = TRUE)

  .cs_baskets <- choices_selected(
    choices = variable_choices(ADAE, subset = .names_baskets),
    selected = .names_baskets
  )

  .cs_scopes <- choices_selected(
    choices = variable_choices(ADAE, subset = .names_scopes),
    selected = .names_scopes,
    fixed = TRUE
  )
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_t_smq(
      label = "Adverse Events by SMQ Table",
      dataname = "ADAE",
      arm_var = choices_selected(
        choices = variable_choices(data[["ADSL"]], subset = c("ARM", "SEX")),
        selected = "ARM"
      ),
      add_total = FALSE,
      baskets = data[[".cs_baskets"]],
      scopes = data[[".cs_scopes"]],
      llt = choices_selected(
        choices = variable_choices(data[["ADAE"]], subset = c("AEDECOD")),
        selected = "AEDECOD"
      ),
      decorators = list(insert_rrow_decorator())
    )
  )
) |> shiny::runApp()
```

</details>

---------

Co-authored-by: Marcin <[email protected]>

R/tm_t_smq.R

@@ -290,8 +290,7 @@ template_smq <- function(dataname,
       all_zero <- function(tr) {
         !inherits(tr, "ContentRow") && rtables::all_zero_or_na(tr)
       }
-      pruned_and_sorted_result <- sorted_result %>% rtables::trim_rows(criteria = all_zero)
-      pruned_and_sorted_result
+      table <- sorted_result %>% rtables::trim_rows(criteria = all_zero)
     }
   )
 
@@ -316,6 +315,14 @@ template_smq <- function(dataname,
 #'
 #' @inherit module_arguments return seealso
 #'
+#' @section Decorating Module:
+#'
+#' This module generates the following objects, which can be modified in place using decorators:
+#' - `table` (`TableTree` - output of `rtables::build_table`)
+#'
+#' For additional details and examples of decorators, refer to the vignette
+#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation.
+#'
 #' @examplesShinylive
 #' library(teal.modules.clinical)
 #' interactive <- function() TRUE
@@ -391,7 +398,8 @@ tm_t_smq <- function(label,
                      scopes,
                      pre_output = NULL,
                      post_output = NULL,
-                     basic_table_args = teal.widgets::basic_table_args()) {
+                     basic_table_args = teal.widgets::basic_table_args(),
+                     decorators = NULL) {
   message("Initializing tm_t_smq")
   checkmate::assert_string(label)
   checkmate::assert_string(dataname)
@@ -408,6 +416,8 @@ tm_t_smq <- function(label,
   checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE)
   checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE)
   checkmate::assert_class(basic_table_args, "basic_table_args")
+  decorators <- normalize_decorators(decorators)
+  assert_decorators(decorators, null.ok = TRUE, "table")
 
   args <- as.list(environment())
 
@@ -432,7 +442,8 @@ tm_t_smq <- function(label,
         na_level = na_level,
         label = label,
         total_label = total_label,
-        basic_table_args = basic_table_args
+        basic_table_args = basic_table_args,
+        decorators = decorators
       )
     ),
     datanames = teal.transform::get_extract_datanames(data_extract_list)
@@ -444,7 +455,6 @@ ui_t_smq <- function(id, ...) {
   ns <- NS(id)
   a <- list(...) # module args
 
-
   is_single_dataset_value <- teal.transform::is_single_dataset(
     a$arm_var,
     a$id_var,
@@ -482,6 +492,7 @@ ui_t_smq <- function(id, ...) {
         data_extract_spec = a$baskets,
         is_single_dataset = is_single_dataset_value
       ),
+      ui_decorate_teal_data(ns("decorator"), decorators = select_decorators(a$decorators, "table")),
       teal.widgets::panel_group(
         teal.widgets::panel_item(
           "Additional Variables Info",
@@ -540,7 +551,8 @@ srv_t_smq <- function(id,
                       na_level,
                       label,
                       total_label,
-                      basic_table_args) {
+                      basic_table_args,
+                      decorators) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI")
   checkmate::assert_class(data, "reactive")
@@ -621,6 +633,7 @@ srv_t_smq <- function(id,
       )
     })
 
+    # Generate r code for the analysis.
     all_q <- reactive({
       validate_checks()
 
@@ -642,18 +655,27 @@ srv_t_smq <- function(id,
       teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls)))
     })
 
+    # Decoration of table output.
+    decorated_table_q <- srv_decorate_teal_data(
+      id = "decorator",
+      data = all_q,
+      decorators = select_decorators(decorators, "table"),
+      expr = table
+    )
+
     # Outputs to render.
-    table_r <- reactive(all_q()[["pruned_and_sorted_result"]])
+    table_r <- reactive(decorated_table_q()[["table"]])
 
     teal.widgets::table_with_settings_srv(
       id = "table",
       table_r = table_r
     )
 
     # Render R code.
+    source_code_r <- reactive(teal.code::get_code(req(decorated_table_q())))
     teal.widgets::verbatim_popup_srv(
       id = "rcode",
-      verbatim_content = reactive(teal.code::get_code(all_q())),
+      verbatim_content = source_code_r,
       title = label
     )
 
@@ -672,7 +694,7 @@ srv_t_smq <- function(id,
           card$append_text("Comment", "header3")
           card$append_text(comment)
         }
-        card$append_src(teal.code::get_code(all_q()))
+        card$append_src(source_code_r())
         card
       }
       teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)