Update forest plots following refactor of g_forest (#911)

# Pull Request  Fixes #910 --------- Signed-off-by: Joe Zhu <sha.joe.zhu@gmail.com> Co-authored-by: Joe Zhu <sha.joe.zhu@gmail.com> Co-authored-by: Davide Garolini <davide.garolini@roche.com>
insightsengineering · Jan 3, 2024 · 3339d51 · 3339d51
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -28,11 +28,12 @@ Depends:
     R (>= 4.0),
     teal (>= 0.14.0.9027),
     teal.transform (>= 0.4.0.9011),
-    tern (>= 0.9.3)
+    tern (>= 0.9.3.9002)
 Imports:
     assertthat,
     broom,
     checkmate,
+    cowplot (>= 0.7.0),
     dplyr,
     DT,
     formatters (>= 0.5.5),
@@ -44,7 +45,7 @@ Imports:
     magrittr,
     methods,
     rlang,
-    rlistings (>= 0.2.4),
+    rlistings (>= 0.2.7),
     rmarkdown,
     rtables (>= 0.6.6),
     scales,

diff --git a/NEWS.md b/NEWS.md
@@ -8,6 +8,7 @@
 * Added parameter `sort_freq_col` to `tm_t_events` to allow the user to select column to use when sorting by decreasing frequency.
 * Added parameter `incl_overall_sum` to `tm_t_events` to allow the user to choose whether overall summary rows are included at the top of the table.
 * Updated the documentation and vignettes to demonstrate method to pass `teal_data` object to `teal::init()`.
+* Updated `tm_g_forest_rsp` and `tm_g_forest_tte` to use refactored version of `g_forest`. Plots are now displayed as `ggplot` objects instead of `grob` objects. Added parameters `font_size` and `rel_width_forest` to control font size and width of plot relative to table, respectively.
 
 ### Bug fixes
 * Fixed bug in `tm_g_lineplot` forcing module to initialize with a table.

diff --git a/R/tm_g_forest_rsp.R b/R/tm_g_forest_rsp.R
@@ -2,6 +2,7 @@
 #'
 #' Creates a valid expression for response forest plot.
 #'
+#' @inheritParams tern::g_forest
 #' @inheritParams template_arguments
 #' @param obj_var_name (`character`)\cr additional text string append to output title.
 #' @param responders (`character`)\cr values of `aval_var` that are considered to be responders.
@@ -34,6 +35,8 @@ template_forest_rsp <- function(dataname = "ANL",
                                 strata_var = NULL,
                                 conf_level = 0.95,
                                 col_symbol_size = NULL,
+                                rel_width_forest = 0.25,
+                                font_size = 15,
                                 ggplot2_args = teal.widgets::ggplot2_args()) {
   assertthat::assert_that(
     assertthat::is.string(dataname),
@@ -43,6 +46,8 @@ template_forest_rsp <- function(dataname = "ANL",
     assertthat::is.string(obj_var_name),
     is.null(subgroup_var) || is.character(subgroup_var)
   )
+  checkmate::assert_number(rel_width_forest, lower = 0, upper = 1)
+  checkmate::assert_number(font_size)
 
   y <- list()
   ref_arm_val <- paste(ref_arm, collapse = "/")
@@ -160,34 +165,55 @@ template_forest_rsp <- 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 best overall response for ", obj_var_name), caption = "")
+      labs = list(
+        title = paste("Forest Plot of Best Overall Response for", obj_var_name),
+        caption = ""
+      )
     )
   )
 
-  plot_call <- substitute(
-    expr = g_forest(
-      tbl = result,
-      col_symbol_size = col_s_size
-    ),
-    env = list(col_s_size = col_symbol_size)
-  )
+  plot_list <- list()
 
-  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)
+  plot_list <- add_expr(
+    plot_list,
+    substitute(
+      expr = {
+        f <- g_forest(
+          tbl = result,
+          col_symbol_size = col_s_size,
+          font_size = font_size,
+          as_list = TRUE
+        )
+      },
+      env = list(
+        col_s_size = col_symbol_size,
+        font_size = font_size
+      )
+    )
   )
 
-  plot_call <- substitute(
-    expr = {
-      p <- plot_call
-      grid::grid.newpage()
-      grid::grid.draw(p)
-    },
-    env = list(plot_call = plot_call)
+  plot_list <- add_expr(
+    plot_list,
+    substitute(
+      expr = {
+        p <- cowplot::plot_grid(
+          f[["table"]] + ggplot2::labs(title = ggplot2_args_title),
+          f[["plot"]] + ggplot2::labs(caption = ggplot2_args_caption),
+          align = "h",
+          axis = "tblr",
+          rel_widths = c(1 - rel_width_forest, rel_width_forest)
+        )
+      },
+      env = list(
+        rel_width_forest = rel_width_forest,
+        ggplot2_args_title = all_ggplot2_args$labs$title,
+        ggplot2_args_caption = all_ggplot2_args$labs$caption
+      )
+    )
   )
 
   # Plot output.
-  y$plot <- plot_call
+  y$plot <- plot_list
 
   y
 }
@@ -196,6 +222,7 @@ template_forest_rsp <- function(dataname = "ANL",
 #'
 #' This teal module produces a grid style Forest plot for response data with `ADaM` structure.
 #'
+#' @inheritParams tern::g_forest
 #' @inheritParams module_arguments
 #' @inheritParams tm_t_binary_outcome
 #' @param fixed_symbol_size (`logical`)\cr
@@ -314,8 +341,10 @@ tm_g_forest_rsp <- function(label,
                             fixed_symbol_size = TRUE,
                             conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order = TRUE),
                             default_responses = c("CR", "PR", "Y", "Complete Response (CR)", "Partial Response (PR)"),
-                            plot_height = c(700L, 200L, 2000L),
-                            plot_width = c(1200L, 800L, 3000L),
+                            plot_height = c(500L, 200L, 2000L),
+                            plot_width = c(1500L, 800L, 3000L),
+                            rel_width_forest = c(25L, 0L, 100L),
+                            font_size = c(15L, 1L, 30L),
                             pre_output = NULL,
                             post_output = NULL,
                             ggplot2_args = teal.widgets::ggplot2_args()) {
@@ -442,7 +471,19 @@ ui_g_forest_rsp <- function(id, ...) {
             multiple = FALSE,
             fixed = a$conf_level$fixed
           ),
-          shiny::checkboxInput(ns("fixed_symbol_size"), "Fixed symbol size", value = TRUE)
+          shiny::checkboxInput(ns("fixed_symbol_size"), "Fixed symbol size", value = TRUE),
+          teal.widgets::optionalSliderInputValMinMax(
+            ns("rel_width_forest"),
+            "Relative Width of Forest Plot (%)",
+            a$rel_width_forest,
+            ticks = FALSE, step = 1
+          ),
+          teal.widgets::optionalSliderInputValMinMax(
+            ns("font_size"),
+            "Table Font Size",
+            a$font_size,
+            ticks = FALSE, step = 1
+          )
         )
       )
     ),
@@ -692,6 +733,8 @@ srv_g_forest_rsp <- function(id,
         strata_var = if (length(strata_var) != 0) strata_var else NULL,
         conf_level = as.numeric(input$conf_level),
         col_symbol_size = `if`(input$fixed_symbol_size, NULL, 1),
+        rel_width_forest = input$rel_width_forest / 100,
+        font_size = input$font_size,
         ggplot2_args = ggplot2_args
       )
 

diff --git a/R/tm_g_forest_tte.R b/R/tm_g_forest_tte.R
@@ -29,13 +29,17 @@ template_forest_tte <- function(dataname = "ANL",
                                 conf_level = 0.95,
                                 col_symbol_size = NULL,
                                 time_unit_var = "AVALU",
+                                rel_width_forest = 0.25,
+                                font_size = 15,
                                 ggplot2_args = teal.widgets::ggplot2_args()) {
   assertthat::assert_that(
     assertthat::is.string(dataname),
     assertthat::is.string(arm_var),
     assertthat::is.string(obj_var_name),
     is.character(subgroup_var) || is.null(subgroup_var)
   )
+  checkmate::assert_number(rel_width_forest, lower = 0, upper = 1)
+  checkmate::assert_number(font_size)
 
   y <- list()
   ref_arm_val <- paste(ref_arm, collapse = "/")
@@ -162,45 +166,59 @@ template_forest_tte <- function(dataname = "ANL",
     user_plot = ggplot2_args,
     module_plot = teal.widgets::ggplot2_args(
       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 "))),
+        title = paste(
+          paste("Forest Plot of Survival Duration for", obj_var_name),
+          ifelse(is.null(strata_var), "", paste("Stratified by", paste(strata_var, collapse = " and "))),
+          sep = "\n"
+        ),
         caption = ""
       )
     )
   )
 
-  plot_call <- substitute(
-    expr = g_forest(
-      tbl = result,
-      col_symbol_size = col_s_size
-    ),
-    env = list(col_s_size = col_symbol_size)
-  )
+  plot_list <- list()
 
-  plot_call <- substitute(
-    decorate_grob(p, titles = title, footnotes = caption, gp_footnotes = grid::gpar(fontsize = 12)),
-    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_list <- add_expr(
+    plot_list,
+    substitute(
+      expr = {
+        f <- g_forest(
+          tbl = result,
+          col_symbol_size = col_s_size,
+          font_size = font_size,
+          as_list = TRUE
+        )
+      },
+      env = list(
+        col_s_size = col_symbol_size,
+        font_size = font_size
+      )
     )
   )
 
-  plot_call <- substitute(
-    env = list(plot_call = plot_call),
-    expr = {
-      p <- plot_call
-      grid::grid.newpage()
-      grid::grid.draw(p)
-    }
+  plot_list <- add_expr(
+    plot_list,
+    substitute(
+      expr = {
+        p <- cowplot::plot_grid(
+          f[["table"]] + ggplot2::labs(title = ggplot2_args_title, subtitle = ggplot2_args_subtitle),
+          f[["plot"]] + ggplot2::labs(caption = ggplot2_args_caption),
+          align = "h",
+          axis = "tblr",
+          rel_widths = c(1 - rel_width_forest, rel_width_forest)
+        )
+      },
+      env = list(
+        rel_width_forest = rel_width_forest,
+        ggplot2_args_title = all_ggplot2_args$labs$title,
+        ggplot2_args_subtitle = all_ggplot2_args$labs$subtitle,
+        ggplot2_args_caption = all_ggplot2_args$labs$caption
+      )
+    )
   )
 
   # Plot output.
-  y$plot <- plot_call
+  y$plot <- plot_list
 
   y
 }
@@ -210,6 +228,7 @@ template_forest_tte <- function(dataname = "ANL",
 #' This teal module produces a grid style Forest plot for time-to-event data
 #' with `ADaM` structure
 #'
+#' @inheritParams tern::g_forest
 #' @inheritParams module_arguments
 #' @inheritParams tm_g_forest_rsp
 #' @param ggplot2_args optional, (`ggplot2_args`)\cr
@@ -271,8 +290,7 @@ template_forest_tte <- function(dataname = "ANL",
 #'       strata_var = choices_selected(
 #'         variable_choices(ADSL, c("STRATA1", "STRATA2")),
 #'         "STRATA2"
-#'       ),
-#'       plot_height = c(600, 200, 2000)
+#'       )
 #'     )
 #'   )
 #' )
@@ -306,8 +324,10 @@ tm_g_forest_tte <- function(label,
                               fixed = TRUE
                             ),
                             fixed_symbol_size = TRUE,
-                            plot_height = c(700L, 200L, 2000L),
-                            plot_width = c(1200L, 800L, 3000L),
+                            plot_height = c(500L, 200L, 2000L),
+                            plot_width = c(1500L, 800L, 3000L),
+                            rel_width_forest = c(25L, 0L, 100L),
+                            font_size = c(15L, 1L, 30L),
                             pre_output = NULL,
                             post_output = NULL,
                             ggplot2_args = teal.widgets::ggplot2_args()) {
@@ -443,6 +463,18 @@ ui_g_forest_tte <- function(id, ...) {
             label = "Time Unit Variable",
             data_extract_spec = a$time_unit_var,
             is_single_dataset = is_single_dataset_value
+          ),
+          teal.widgets::optionalSliderInputValMinMax(
+            ns("rel_width_forest"),
+            "Relative Width of Forest Plot (%)",
+            a$rel_width_forest,
+            ticks = FALSE, step = 1
+          ),
+          teal.widgets::optionalSliderInputValMinMax(
+            ns("font_size"),
+            "Table Font Size",
+            a$font_size,
+            ticks = FALSE, step = 1
           )
         )
       )
@@ -624,6 +656,8 @@ srv_g_forest_tte <- function(id,
         conf_level = as.numeric(input$conf_level),
         col_symbol_size = if (!input$fixed_symbol_size) 1,
         time_unit_var = as.vector(anl_m$columns_source$time_unit_var),
+        rel_width_forest = input$rel_width_forest / 100,
+        font_size = input$font_size,
         ggplot2_args = ggplot2_args
       )
       teal.code::eval_code(anl_q(), as.expression(my_calls))

diff --git a/man/template_forest_rsp.Rd b/man/template_forest_rsp.Rd
diff --git a/man/template_forest_tte.Rd b/man/template_forest_tte.Rd