Merge pull request #118 from Merck/Add-example-of-long-treatment-labels

Add example of long treatment labels

Author: wangben718

.github/workflows/test-coverage.yaml

@@ -23,7 +23,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage

R/format_ae_forestly.R

@@ -253,7 +253,13 @@ format_ae_forestly <- function(
   columnGroups <- list()
   for (i in 1:m_group) {
     columnGroups[[i]] <- reactable::colGroup(
-      name = paste0(outdata$group[i], "<br> (N=", outdata$n_pop[i], ")"),
+      name = paste0(
+        '<span title="',
+        paste0(outdata$group[i], " (N=", outdata$n_pop[i], ")"),
+        '">',
+        paste0(outdata$group[i], "<br> (N=", outdata$n_pop[i], ")"),
+        '</span>'
+      ),
       html = TRUE,
       columns = c(name_n[i], name_prop[i])
     )

vignettes/customize-width.Rmd

@@ -24,11 +24,14 @@ knitr::opts_chunk$set(
 ```{r}
 library(forestly)
 library(metalite)
+library(dplyr)
 ```
 
 The interactive AE forest plots include AE-specific tables presenting numerical values for AE proportions, differences, and confidence intervals (CI), alongside their visualizations. Each type of information is displayed in a separate column. In this vignette, we demonstrate how to customize the column widths in these tables.
 
-# Step 1: build your metadata
+# General Use
+
+## Step 1: build your metadata
 
 Building interactive AE forest plots starts with constructing the metadata. The detailed procedure for building metadata is covered in the vignette [Generate Interactive AE Forest Plots with Drill Down to AE Listing](https://merck.github.io/forestly/articles/forestly.html). Therefore, in this vignette, we will skip those details and directly use the metadata created there. 
 
@@ -77,7 +80,7 @@ meta <- meta_adam(population = adsl, observation = adae) |>
 ```
 
 
-# Step 2: adjusting column widths
+## Step 2: adjusting column widths
 
 Users can control the column widths using the following arguments:
 
@@ -106,3 +109,96 @@ meta |>
   ) |>
   ae_forestly()
 ```
+
+# Multiple, Long Treatment Labels Example
+
+## Step 1: build example metadata
+
+The datasets used here include five treatment arms with long labels.
+
+```{r}
+adsl <- forestly_adsl
+adae <- forestly_adae
+
+set.seed(1234)
+adsl$TRTA <- sample(
+  x = c("Control Arm A",
+        "Control Arm B",
+        "Active Arm (Mono): Drug X",
+        "Active Arm (Comb): Drug X + Drug A + Drug B + Drug C",
+        "Active Arm: Cumulative Drug X"),
+  size = nrow(adsl),
+  replace = TRUE
+)
+adae <- adae |> 
+  dplyr::select(-TRTA) |>
+  dplyr::left_join(
+    adsl,
+    by = c("USUBJID"),
+    suffix = c("", ".y")
+  ) |>
+  dplyr::select(-ends_with(".y"))
+
+adsl$TRTA <- factor(
+  adsl$TRTA,
+  levels = c("Active Arm: Cumulative Drug X",
+             "Active Arm (Mono): Drug X",
+             "Active Arm (Comb): Drug X + Drug A + Drug B + Drug C",
+             "Control Arm A",
+             "Control Arm B")
+)
+adae$TRTA <- factor(
+  adae$TRTA,
+  levels = c("Active Arm: Cumulative Drug X",
+             "Active Arm (Mono): Drug X",
+             "Active Arm (Comb): Drug X + Drug A + Drug B + Drug C",
+             "Control Arm A",
+             "Control Arm B")
+)
+
+meta <- meta_adam(population = adsl, observation = adae) |>
+  define_plan(plan = plan(
+    analysis = "ae_forestly",
+    population = "apat",
+    observation = "apat",
+    parameter = "any;drug-related"
+  )) |>
+  define_analysis(name = "ae_forestly", label = "Interactive Forest Plot") |>
+  define_population(
+    name = "apat", group = "TRTA", id = "USUBJID",
+    subset = SAFFL == "Y", label = "All Patient as Treated"
+  ) |>
+  define_observation(
+    name = "apat", group = "TRTA",
+    subset = SAFFL == "Y", label = "All Patient as Treated"
+  ) |>
+  define_parameter(
+    name = "any",
+    subset = NULL,
+    label = "Any AEs",
+    var = "AEDECOD", soc = "AEBODSYS"
+  ) |>
+  define_parameter(
+    name = "drug-related",
+    subset = toupper(AREL) == "RELATED",
+    label = "Drug-related AEs",
+    var = "AEDECOD", soc = "AEBODSYS"
+  ) |>
+  meta_build()
+```
+
+## Step 2: adjusting column widths
+
+In this example, we adjust the column widths to accommodate the long treatment labels and multiple treatment arms. To ensure sufficient space for the legend, the `width_fig` is set to a larger value and the `footer_space` is increased.
+
+```{r}
+meta |>
+  prepare_ae_forestly() |>
+  format_ae_forestly(
+    footer_space = 210,
+    width_fig = 420,
+    display = c("n", "prop", "fig_prop", "fig_diff", "diff"),
+    color = c("#66203A", "#00857C", "#6ECEB2", "#BFED33", "#DFEd31")
+  ) |>
+  ae_forestly()
+```