introduce transformators parameter

insightsengineering · Jan 21, 2025 · 02d7e41 · 02d7e41
1 parent 4f07c33
commit 02d7e41
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Showing 17 changed files with 73 additions and 17 deletions.
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.
 #'
@@ -56,7 +57,8 @@ 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)
@@ -90,6 +92,7 @@ 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.
 #'
@@ -59,7 +60,8 @@ 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)
@@ -90,6 +92,7 @@ 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/sampleVarSpecServer.Rd b/man/sampleVarSpecServer.Rd
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
diff --git a/man/tm_g_quality.Rd b/man/tm_g_quality.Rd
diff --git a/man/tm_g_scatterplot.Rd b/man/tm_g_scatterplot.Rd
diff --git a/man/tm_g_volcanoplot.Rd b/man/tm_g_volcanoplot.Rd