Merge branch 'main' into 1301-feature-request-add-confidence-interval…

…s-for-quantiles-in-surv_time

.github/workflows/check.yaml

@@ -25,6 +25,11 @@ jobs:
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/nestcolor
+        insightsengineering/rtables
+        insightsengineering/formatters
       additional-env-vars: |
         _R_CHECK_CRAN_INCOMING_REMOTE_=false
       additional-r-cmd-check-params: --as-cran
@@ -46,6 +51,11 @@ jobs:
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/nestcolor
+        insightsengineering/rtables
+        insightsengineering/formatters
       additional-env-vars: |
         _R_CHECK_CRAN_INCOMING_REMOTE_=false
         NOT_CRAN=true
@@ -69,6 +79,11 @@ jobs:
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/nestcolor
+        insightsengineering/rtables
+        insightsengineering/formatters
       additional-env-vars: |
         NOT_CRAN=true
   linter:
@@ -81,6 +96,11 @@ jobs:
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/nestcolor
+        insightsengineering/rtables
+        insightsengineering/formatters
       auto-update: true
   gitleaks:
     name: gitleaks 💧

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: tern
 Title: Create Common TLGs Used in Clinical Trials
-Version: 0.9.6.9010
-Date: 2024-10-25
+Version: 0.9.6.9012
+Date: 2024-11-01
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre")),
     person("Daniel", "Sabanés Bové", , "[email protected]", role = "aut"),

NEWS.md

@@ -1,10 +1,15 @@
-# tern 0.9.6.9010
+# tern 0.9.6.9012
 
 ### Enhancements
 * Added the `denom` parameter to `s_count_cumulative()`, `s_count_missed_doses()`, and `s_count_occurrences_by_grade()`.
 * Added `"N_row"` as an optional input to `denom` in `s_count_occurrences()`.
 * Refactored `a_count_occurrences_by_grade()` to no longer use `make_afun()`.
 
+### Enhancements
+* Added `rel_height_plot` parameter to `g_lineplot()` to control the line plot height relative to annotation table height.
+* Updated the `table_font_size` parameter of `g_lineplot()` to control the size of all text in the annotation table, including labels.
+* Added `as_list` parameter to `g_lineplot()` to allow users to return the line plot and annotation table elements as a list instead of stacked for more complex customization.
+
 ### Bug Fixes
 * Fixed bug in `a_summary()` causing non-unique `row_name` values to occur when multiple statistics are selected for count variables.
 

R/g_lineplot.R

@@ -2,7 +2,7 @@
 #'
 #' @description `r lifecycle::badge("stable")`
 #'
-#' Line plot with the optional table.
+#' Line plot with optional table.
 #'
 #' @inheritParams argument_convention
 #' @param alt_counts_df (`data.frame` or `NULL`)\cr data set that will be used (only)
@@ -72,6 +72,11 @@
 #' @param col (`character`)\cr color(s). See `?ggplot2::aes_colour_fill_alpha` for example values.
 #' @param linetype (`character`)\cr line type(s). See `?ggplot2::aes_linetype_size_shape` for example values.
 #' @param errorbar_width (`numeric(1)`)\cr width of the error bars.
+#' @param rel_height_plot (`proportion`)\cr proportion of total figure height to allocate to the line plot.
+#'   Relative height of annotation table is then `1 - rel_height_plot`. If `table = NULL`, this parameter is ignored.
+#' @param as_list (`flag`)\cr whether the two `ggplot` objects should be returned as a list when `table` is not `NULL`.
+#'   If `TRUE`, a named list with two elements, `plot` and `table`, will be returned. If `FALSE` (default) the
+#'   annotation table is printed below the plot via [cowplot::plot_grid()].
 #'
 #' @return A `ggplot` line plot (and statistics table if applicable).
 #'
@@ -162,7 +167,9 @@ g_lineplot <- function(df,
                        errorbar_width = 0.45,
                        newpage = lifecycle::deprecated(),
                        col = NULL,
-                       linetype = NULL) {
+                       linetype = NULL,
+                       rel_height_plot = 0.5,
+                       as_list = FALSE) {
   checkmate::assert_character(variables, any.missing = TRUE)
   checkmate::assert_character(mid, null.ok = TRUE)
   checkmate::assert_character(interval, null.ok = TRUE)
@@ -174,6 +181,8 @@ g_lineplot <- function(df,
   checkmate::assert_number(errorbar_width, lower = 0)
   checkmate::assert_string(title, null.ok = TRUE)
   checkmate::assert_string(subtitle, null.ok = TRUE)
+  assert_proportion_value(rel_height_plot)
+  checkmate::assert_logical(as_list)
 
   if (!is.null(table)) {
     table_format <- get_formats_from_stats(table)
@@ -462,9 +471,15 @@ g_lineplot <- function(df,
         axis.ticks = ggplot2::element_blank(),
         axis.title = ggplot2::element_blank(),
         axis.text.x = ggplot2::element_blank(),
-        axis.text.y = ggplot2::element_text(margin = ggplot2::margin(t = 0, r = 0, b = 0, l = 5)),
+        axis.text.y = ggplot2::element_text(
+          size = table_font_size * ggplot2::.pt,
+          margin = ggplot2::margin(t = 0, r = 0, b = 0, l = 5)
+        ),
         strip.text = ggplot2::element_text(hjust = 0),
-        strip.text.x = ggplot2::element_text(margin = ggplot2::margin(1.5, 0, 1.5, 0, "pt")),
+        strip.text.x = ggplot2::element_text(
+          size = table_font_size * ggplot2::.pt,
+          margin = ggplot2::margin(1.5, 0, 1.5, 0, "pt")
+        ),
         strip.background = ggplot2::element_rect(fill = "grey95", color = NA),
         legend.position = "none"
       )
@@ -473,8 +488,19 @@ g_lineplot <- function(df,
       tbl <- tbl + ggplot2::facet_wrap(facets = group_var, ncol = 1)
     }
 
-    # align plot and table
-    cowplot::plot_grid(p, tbl, ncol = 1, align = "v", axis = "tblr")
+    if (!as_list) {
+      # align plot and table
+      cowplot::plot_grid(
+        p,
+        tbl,
+        ncol = 1,
+        align = "v",
+        axis = "tblr",
+        rel_heights = c(rel_height_plot, 1 - rel_height_plot)
+      )
+    } else {
+      list(plot = p, table = tbl)
+    }
   } else {
     p
   }