588 Add "Stratified by" Subtitles (#594)

* Add subtitle to tm_g_forest_tte * Add subtitle to tm_t_coxreg * Add subtitle to tm_t_binary_outcome * Update NEWS * Update tests * [skip actions] Restyle files * [skip actions] Roxygen Man Pages Auto Update * Fix test for tm_g_forest_tte Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
insightsengineering · Sep 16, 2022 · 86f7f04 · 86f7f04
1 parent 697afbf
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diff --git a/NEWS.md b/NEWS.md
@@ -73,6 +73,7 @@
 * `tm_t_events_summary` now allows nested `arm_var` columns matching other outputs such as `tm_t_events`.
 * Added validation in `tm_t_abnormality_by_worst_grade` when `arm_var` is not selected.
 * Enhanced `tm_t_binary_outcome` to include all responders in the response table by default.
+* Added a subtitle to `tm_g_forest_tte`, `tm_t_coxreg`, and `tm_t_binary_outcome` listing stratification factors.
 
 ### Bug fixes
 * Fixed a bug to prevent processing of empty sets of data by `tm_g_forest_rsp.R` causing `shiny` errors during the runtime.

diff --git a/R/tm_g_forest_tte.R b/R/tm_g_forest_tte.R
@@ -161,7 +161,11 @@ template_forest_tte <- function(dataname = "ANL",
   all_ggplot2_args <- teal.widgets::resolve_ggplot2_args(
     user_plot = ggplot2_args,
     module_plot = teal.widgets::ggplot2_args(
-      labs = list(title = paste0("Forest plot of survival duration for ", obj_var_name), caption = "")
+      labs = list(
+        title = paste("Forest Plot of Survival Duration for", obj_var_name),
+        subtitle = ifelse(is.null(strata_var), "", paste("Stratified by", paste(strata_var, collapse = " and "))),
+        caption = ""
+      )
     )
   )
 
@@ -175,7 +179,15 @@ template_forest_tte <- function(dataname = "ANL",
 
   plot_call <- substitute(
     decorate_grob(p, titles = title, footnotes = caption, gp_footnotes = grid::gpar(fontsize = 12)),
-    env = list(title = all_ggplot2_args$labs$title, caption = all_ggplot2_args$labs$caption, p = plot_call)
+    env = list(
+      title = `if`(
+        all_ggplot2_args$labs$subtitle == "",
+        all_ggplot2_args$labs$title,
+        c(all_ggplot2_args$labs$title, all_ggplot2_args$labs$subtitle)
+      ),
+      caption = all_ggplot2_args$labs$caption,
+      p = plot_call
+    )
   )
 
   plot_call <- substitute(

diff --git a/R/tm_t_binary_outcome.R b/R/tm_t_binary_outcome.R
@@ -153,10 +153,16 @@ template_binary_outcome <- function(dataname,
     paste("Table of", paramcd, "for", responder_val, "Responders")
   }
 
+  strata_var <- control$strat$strat
+  subtitle <- ifelse(length(strata_var) == 0, "", paste("Stratified by", paste(strata_var, collapse = " and ")))
+
   parsed_basic_table_args <- teal.widgets::parse_basic_table_args(
     teal.widgets::resolve_basic_table_args(
       user_table = basic_table_args,
-      module_table = teal.widgets::basic_table_args(title = table_title)
+      module_table = teal.widgets::basic_table_args(
+        title = table_title,
+        subtitles = subtitle
+      )
     )
   )
 

diff --git a/R/tm_t_coxreg.R b/R/tm_t_coxreg.R
@@ -25,7 +25,7 @@ template_coxreg_u <- function(dataname,
                               control = control_coxreg(),
                               append = FALSE,
                               basic_table_args = teal.widgets::basic_table_args(
-                                title = paste0("Multi-Variable Cox Regression for ", paramcd)
+                                title = paste("Multi-Variable Cox Regression for", paramcd)
                               )) {
   y <- list()
   ref_arm_val <- paste(ref_arm, collapse = "/")
@@ -972,12 +972,17 @@ srv_t_coxreg <- function(id,
       ANL <- teal.code::chunks_get_var("ANL") # nolint
       paramcd <- as.character(unique(ANL[[unlist(paramcd$filter)["vars_selected"]]]))
       multivariate <- input$type == "Multivariate"
+      strata_var <- as.vector(anl_m$columns_source$strata_var)
 
       if (input$type == "Multivariate") {
-        main_title <- paste0("Multi-Variable Cox Regression for ", paramcd)
+        main_title <- paste("Multi-Variable Cox Regression for", paramcd)
+        subtitle <- ifelse(length(strata_var) == 0, "", paste("Stratified by", paste(strata_var, collapse = " and ")))
         all_basic_table_args <- teal.widgets::resolve_basic_table_args(
           user_table = basic_table_args,
-          module_table = teal.widgets::basic_table_args(title = main_title)
+          module_table = teal.widgets::basic_table_args(
+            title = main_title,
+            subtitles = subtitle
+          )
         )
         expr <- call_template(unlist(input$buckets$Comp), anl_m, paramcd, multivariate, all_basic_table_args)
         mapply(
@@ -988,10 +993,14 @@ srv_t_coxreg <- function(id,
         teal.code::chunks_safe_eval()
         teal.code::chunks_get_var("result")
       } else {
-        main_title <- paste0("Cox Regression for ", paramcd)
+        main_title <- paste("Cox Regression for", paramcd)
+        subtitle <- ifelse(length(strata_var) == 0, "", paste("Stratified by", paste(strata_var, collapse = " and ")))
         all_basic_table_args <- teal.widgets::resolve_basic_table_args(
           user_table = basic_table_args,
-          module_table = teal.widgets::basic_table_args(title = main_title)
+          module_table = teal.widgets::basic_table_args(
+            title = main_title,
+            subtitles = subtitle
+          )
         )
         teal.code::chunks_push(expression = quote(result <- list()), id = "result_initiation_call")
         lapply(unlist(input$buckets$Comp), function(x) {

diff --git a/man/template_coxreg_u.Rd b/man/template_coxreg_u.Rd
diff --git a/tests/testthat/test-tm_g_forest_tte.R b/tests/testthat/test-tm_g_forest_tte.R
@@ -53,12 +53,14 @@ testthat::test_that("template_forest_tte generates correct expressions", {
     }),
     plot = quote({
       p <- decorate_grob(g_forest(tbl = result, col_symbol_size = NULL),
-        titles = "Forest plot of survival duration for ", footnotes = "",
-        gp_footnotes = grid::gpar(fontsize = 12)
+        titles = c(),
+        footnotes = "", gp_footnotes = grid::gpar(fontsize = 12)
       )
       grid::grid.newpage()
       grid::grid.draw(p)
     })
   )
+  expected$plot[[2]][[3]]$titles <- c("Forest Plot of Survival Duration for ", "Stratified by STRATA2")
+
   testthat::expect_equal(result, expected)
 })
diff --git a/tests/testthat/test-tm_t_binary_outcome.R b/tests/testthat/test-tm_t_binary_outcome.R
@@ -28,7 +28,8 @@ testthat::test_that("template_binary_outcome generates standard expressions", {
     }),
     layout = quote(
       lyt <- rtables::basic_table(
-        title = "Table of BESRSPI for Complete Response (CR) and Partial Response (PR) Responders"
+        title = "Table of BESRSPI for Complete Response (CR) and Partial Response (PR) Responders",
+        subtitles = ""
       ) %>%
         rtables::split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
         rtables::add_colcounts() %>%
@@ -101,7 +102,10 @@ testthat::test_that("template_binary_outcome generates right expressions with no
         df_explicit_na()
     }),
     layout = quote(
-      lyt <- rtables::basic_table(title = "Table of BESRSPI for PR and SD Responders") %>%
+      lyt <- rtables::basic_table(
+        title = "Table of BESRSPI for PR and SD Responders",
+        subtitles = ""
+      ) %>%
         rtables::split_cols_by(var = "ARM", ref_group = "B: Placebo") %>%
         rtables::add_colcounts() %>%
         estimate_proportion(
@@ -163,7 +167,8 @@ testthat::test_that("template_binary_outcome generates expression without arm co
     }),
     layout = quote(
       lyt <- rtables::basic_table(
-        title = "Table of BESRSPI for Complete Response (CR) and Partial Response (PR) Responders"
+        title = "Table of BESRSPI for Complete Response (CR) and Partial Response (PR) Responders",
+        subtitles = ""
       ) %>%
         rtables::split_cols_by(var = "ARM") %>%
         rtables::add_colcounts() %>%
@@ -219,7 +224,8 @@ testthat::test_that("template_binary_outcome generates expression with non-defau
     }),
     layout = quote(
       lyt <- rtables::basic_table(
-        title = "Table of BESRSPI for Complete Response (CR) and Partial Response (PR) Responders"
+        title = "Table of BESRSPI for Complete Response (CR) and Partial Response (PR) Responders",
+        subtitles = "Stratified by SEX"
       ) %>%
         rtables::split_cols_by(var = "ARM", ref_group = "B: Placebo") %>%
         rtables::add_colcounts() %>%
@@ -311,7 +317,8 @@ testthat::test_that("template_binary_outcome can combine comparison arms", {
     ),
     layout = quote(
       lyt <- rtables::basic_table(
-        title = "Table of BESRSPI for Complete Response (CR) and Partial Response (PR) Responders"
+        title = "Table of BESRSPI for Complete Response (CR) and Partial Response (PR) Responders",
+        subtitles = ""
       ) %>%
         split_cols_by_groups(
           var = "ARMCD", groups_list = groups, ref_group = names(groups)[1]
@@ -385,7 +392,8 @@ testthat::test_that("template_binary_outcome can combine comparison arms when co
     }),
     layout = quote(
       lyt <- rtables::basic_table(
-        title = "Table of BESRSPI for Complete Response (CR) and Partial Response (PR) Responders"
+        title = "Table of BESRSPI for Complete Response (CR) and Partial Response (PR) Responders",
+        subtitles = ""
       ) %>%
         rtables::split_cols_by(var = "ARMCD") %>%
         rtables::add_colcounts() %>%
@@ -454,7 +462,8 @@ testthat::test_that("template_binary_outcome can combine refs", {
     }),
     layout = quote(
       lyt <- rtables::basic_table(
-        title = "Table of BESRSPI for Complete Response (CR) and Partial Response (PR) Responders"
+        title = "Table of BESRSPI for Complete Response (CR) and Partial Response (PR) Responders",
+        subtitles = ""
       ) %>%
         rtables::split_cols_by(var = "ARMCD", ref_group = "ARM A/ARM B") %>%
         rtables::add_colcounts() %>%