1441 Introduce transformators parameter in modules (#399)

insightsengineering/teal#1441 Included `transformators` parameter in modules. This is passed to `teal::module` that does assertions and checks on this parameter. --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
insightsengineering · Jan 24, 2025 · 8005f31 · 8005f31
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commit 8005f31
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Showing 18 changed files with 95 additions and 27 deletions.
diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml
@@ -38,6 +38,8 @@ jobs:
       strategy: ${{ matrix.test-strategy }}
       additional-env-vars: |
         PKG_SYSREQS_DRY_RUN=true
+      extra-deps: |
+        teal.slice (>= 0.5.1.9024),teal.code (>= 0.5.0.9022)
   branch-cleanup:
     if: >
       github.event_name == 'schedule' || (

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -33,27 +33,27 @@ Depends:
     ggplot2,
     R (>= 4.1),
     shiny,
-    teal (>= 0.15.0)
+    teal (>= 0.15.2.9103)
 Imports:
     checkmate,
     DT,
     edgeR,
     forcats,
     hermes (>= 1.7.1),
     lifecycle,
-    MultiAssayExperiment,
-    rtables (>= 0.5.1),
+    MultiAssayExperiment (>= 1.32.0),
+    rtables (>= 0.6.11),
     S4Vectors,
     shinyRadioMatrix (>= 0.2.1),
     shinyWidgets,
     stats,
     stringr,
-    SummarizedExperiment,
-    teal.data (>= 0.3.0.9018),
-    teal.logger (>= 0.3.0.9003),
-    teal.reporter (>= 0.2.0),
-    teal.widgets (>= 0.4.0),
-    tern (>= 0.7.10),
+    SummarizedExperiment (>= 1.36.0),
+    teal.data (>= 0.6.0.9025),
+    teal.logger (>= 0.3.0.9004),
+    teal.reporter (>= 0.3.1.9023),
+    teal.widgets (>= 0.4.2.9025),
+    tern (>= 0.9.7),
     utils
 Suggests:
     BiocStyle,
@@ -66,14 +66,24 @@ Suggests:
     R6,
     rmarkdown,
     rvest,
-    shinytest2 (>= 0.2.0),
-    testthat (>= 2.0)
+    shinytest2 (>= 0.3.2),
+    testthat (>= 3.1.5)
 VignetteBuilder:
     knitr
 RdMacros:
     lifecycle
 biocViews:
 Config/Needs/website: insightsengineering/nesttemplate
+Config/Needs/verdepcheck: tidyverse/ggplot2, rstudio/shiny,
+    insightsengineering/teal, insightsengineering/teal.slice, insightsengineering/teal.code, 
+    insightsengineering/teal.transform,
+    mllg/checkmate, bioc::edgeR, rstudio/DT, tidyverse/forcats, insightsengineering/hermes, 
+    r-lib/lifecycle,  bioc::MultiAssayExperiment, insightsengineering/rtables, bioc::S4Vectors,
+    antonmalko/shinyRadioMatrix, dreamRs/shinyWidgets, tidyverse/stringr, bioc::SummarizedExperiment,
+    insightsengineering/teal.data, insightsengineering/teal.logger, insightsengineering/teal.reporter,
+    insightsengineering/teal.widgets, insightsengineering/tern, bioc::BiocStyle, r-lib/covr,
+    tidyverse/dplyr, futureverse/globals, yihui/knitr, daroczig/logger, HenrikBengtsson/matrixStats,
+    r-lib/R6, rstudio/rmarkdown, tidyverse/rvest, rstudio/shinytest2, r-lib/testthat
 Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US

diff --git a/R/barplot.R b/R/barplot.R
@@ -6,6 +6,7 @@
 #' analysis.
 #'
 #' @inheritParams module_arguments
+#' @inheritParams teal::module
 #'
 #' @return Shiny module to be used in the teal app.
 #'
@@ -35,7 +36,8 @@ tm_g_barplot <- function(label,
                          ),
                          pre_output = NULL,
                          post_output = NULL,
-                         .test = FALSE) {
+                         .test = FALSE,
+                         transformators = list()) {
   message("Initializing tm_g_barplot")
   assert_string(label)
   assert_string(mae_name)
@@ -62,6 +64,7 @@ tm_g_barplot <- function(label,
       post_output = post_output,
       .test = .test
     ),
+    transformators = transformators,
     datanames = mae_name
   )
 }

diff --git a/R/boxplot.R b/R/boxplot.R
@@ -6,6 +6,7 @@
 #' analysis.
 #'
 #' @inheritParams module_arguments
+#' @inheritParams teal::module
 #'
 #' @return Shiny module to be used in the teal app.
 #'
@@ -36,7 +37,8 @@ tm_g_boxplot <- function(label,
                          ),
                          pre_output = NULL,
                          post_output = NULL,
-                         .test = FALSE) {
+                         .test = FALSE,
+                         transformators = list()) {
   message("Initializing tm_g_boxplot")
   assert_string(label)
   assert_string(mae_name)
@@ -63,6 +65,7 @@ tm_g_boxplot <- function(label,
       post_output = post_output,
       .test = .test
     ),
+    transformators = transformators,
     datanames = mae_name
   )
 }

diff --git a/R/forestplot.R b/R/forestplot.R
@@ -5,6 +5,7 @@
 #' This module provides an interactive survival forest plot.
 #'
 #' @inheritParams module_arguments
+#' @inheritParams teal::module
 #'
 #' @return Shiny module to be used in the teal app.
 #'
@@ -54,7 +55,8 @@ tm_g_forest_tte <- function(label,
                             post_output = NULL,
                             plot_height = c(600L, 200L, 2000L),
                             plot_width = c(1360L, 500L, 2000L),
-                            .test = FALSE) {
+                            .test = FALSE,
+                            transformators = list()) {
   message("Initializing tm_g_forest_tte")
   assert_string(label)
   assert_string(adtte_name)
@@ -88,6 +90,7 @@ tm_g_forest_tte <- function(label,
       post_output = post_output,
       .test = .test
     ),
+    transformators = transformators,
     datanames = c(adtte_name, mae_name)
   )
 }

diff --git a/R/km.R b/R/km.R
@@ -6,6 +6,7 @@
 #' `ADaM` structure.
 #'
 #' @inheritParams module_arguments
+#' @inheritParams teal::module
 #'
 #' @return Shiny module to be used in the teal app.
 #'
@@ -57,7 +58,8 @@ tm_g_km <- function(label,
                     ),
                     pre_output = NULL,
                     post_output = NULL,
-                    .test = FALSE) {
+                    .test = FALSE,
+                    transformators = list()) {
   message("Initializing tm_g_km")
   assert_string(label)
   assert_string(adtte_name)
@@ -88,6 +90,7 @@ tm_g_km <- function(label,
       post_output = post_output,
       .test = .test
     ),
+    transformators = transformators,
     datanames = c(adtte_name, mae_name)
   )
 }

diff --git a/R/pca.R b/R/pca.R
@@ -7,6 +7,7 @@
 #' variables.
 #'
 #' @inheritParams module_arguments
+#' @inheritParams teal::module
 #'
 #' @return Shiny module to be used in the teal app.
 #' @export
@@ -30,7 +31,8 @@ tm_g_pca <- function(label,
                      exclude_assays = character(),
                      pre_output = NULL,
                      post_output = NULL,
-                     .test = FALSE) {
+                     .test = FALSE,
+                     transformators = list()) {
   message("Initializing tm_g_pca")
   assert_string(label)
   assert_string(mae_name)
@@ -52,6 +54,7 @@ tm_g_pca <- function(label,
       post_output = post_output,
       .test = .test
     ),
+    transformators = transformators,
     datanames = mae_name
   )
 }

diff --git a/R/quality.R b/R/quality.R
@@ -60,6 +60,7 @@ heatmap_plot <- function(object, assay_name) {
 #' for RNA-seq gene expression quality control.
 #'
 #' @inheritParams module_arguments
+#' @inheritParams teal::module
 #'
 #' @return Shiny module to be used in the teal app.
 #'
@@ -84,7 +85,8 @@ tm_g_quality <- function(label,
                          exclude_assays = character(),
                          pre_output = NULL,
                          post_output = NULL,
-                         .test = FALSE) {
+                         .test = FALSE,
+                         transformators = list()) {
   assert_string(label)
   assert_string(mae_name)
   assert_character(exclude_assays, any.missing = FALSE)
@@ -106,6 +108,7 @@ tm_g_quality <- function(label,
       post_output = post_output,
       .test = .test
     ),
+    transformators = transformators,
     datanames = mae_name
   )
 }

diff --git a/R/scatterplot.R b/R/scatterplot.R
@@ -6,6 +6,7 @@
 #' analysis.
 #'
 #' @inheritParams module_arguments
+#' @inheritParams teal::module
 #'
 #' @return Shiny module to be used in the teal app.
 #'
@@ -35,7 +36,8 @@ tm_g_scatterplot <- function(label,
                              ),
                              pre_output = NULL,
                              post_output = NULL,
-                             .test = FALSE) {
+                             .test = FALSE,
+                             transformators = list()) {
   message("Initializing tm_g_scatterplot")
   assert_string(label)
   assert_string(mae_name)
@@ -61,6 +63,7 @@ tm_g_scatterplot <- function(label,
       post_output = post_output,
       .test = .test
     ),
+    transformators = transformators,
     datanames = mae_name
   )
 }

diff --git a/R/volcanoplot.R b/R/volcanoplot.R
@@ -6,6 +6,7 @@
 #' analysis.
 #'
 #' @inheritParams module_arguments
+#' @inheritParams teal::module
 #'
 #' @return Shiny module to be used in the teal app.
 #'
@@ -30,7 +31,8 @@ tm_g_volcanoplot <- function(label,
                              exclude_assays = character(),
                              pre_output = NULL,
                              post_output = NULL,
-                             .test = FALSE) {
+                             .test = FALSE,
+                             transformators = list()) {
   message("Initializing tm_g_volcanoplot")
   assert_string(label)
   assert_string(mae_name)
@@ -53,6 +55,7 @@ tm_g_volcanoplot <- function(label,
       post_output = post_output,
       .test = .test
     ),
+    transformators = transformators,
     datanames = mae_name
   )
 }

diff --git a/man/tm_g_barplot.Rd b/man/tm_g_barplot.Rd
diff --git a/man/tm_g_boxplot.Rd b/man/tm_g_boxplot.Rd
diff --git a/man/tm_g_forest_tte.Rd b/man/tm_g_forest_tte.Rd
diff --git a/man/tm_g_km.Rd b/man/tm_g_km.Rd
diff --git a/man/tm_g_pca.Rd b/man/tm_g_pca.Rd