1441 Introduce transformators parameter in modules

R/tm_a_pca.R

@@ -133,7 +133,8 @@ tm_a_pca <- function(label = "Principal Component Analysis",
                      size = c(2, 1, 8),
                      pre_output = NULL,
                      post_output = NULL,
-                     decorators = NULL) {
+                     transformators = list(),
+                     decorators = list()) {
   message("Initializing tm_a_pca")
 
   # Normalize the parameters
@@ -186,7 +187,7 @@ tm_a_pca <- function(label = "Principal Component Analysis",
 
   available_decorators <- c("elbow_plot", "circle_plot", "biplot", "eigenvector_plot")
   decorators <- normalize_decorators(decorators)
-  assert_decorators(decorators, null.ok = TRUE, available_decorators)
+  assert_decorators(decorators, available_decorators)
   # End of assertions
 
   # Make UI args
@@ -208,6 +209,7 @@ tm_a_pca <- function(label = "Principal Component Analysis",
         decorators = decorators
       )
     ),
+    transformators = transformators,
     datanames = teal.transform::get_extract_datanames(data_extract_list)
   )
   attr(ans, "teal_bookmarkable") <- FALSE

R/tm_a_regression.R

@@ -157,7 +157,8 @@ tm_a_regression <- function(label = "Regression Analysis",
                             default_plot_type = 1,
                             default_outlier_label = "USUBJID",
                             label_segment_threshold = c(0.5, 0, 10),
-                            decorators = NULL) {
+                            transformators = list(),
+                            decorators = list()) {
   message("Initializing tm_a_regression")
 
   # Normalize the parameters
@@ -211,7 +212,7 @@ tm_a_regression <- function(label = "Regression Analysis",
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
   checkmate::assert_choice(default_plot_type, seq.int(1L, length(plot_choices)))
   checkmate::assert_string(default_outlier_label)
-  checkmate::assert_list(decorators, "teal_transform_module", null.ok = TRUE)
+  checkmate::assert_list(decorators, "teal_transform_module")
 
   if (length(label_segment_threshold) == 1) {
     checkmate::assert_numeric(label_segment_threshold, any.missing = FALSE, finite = TRUE)
@@ -225,7 +226,7 @@ tm_a_regression <- function(label = "Regression Analysis",
     )
   }
   decorators <- normalize_decorators(decorators)
-  assert_decorators(decorators, "plot", null.ok = TRUE)
+  assert_decorators(decorators, "plot")
   # End of assertions
 
   # Make UI args
@@ -251,6 +252,7 @@ tm_a_regression <- function(label = "Regression Analysis",
         decorators = decorators
       )
     ),
+    transformators = transformators,
     datanames = teal.transform::get_extract_datanames(data_extract_list)
   )
   attr(ans, "teal_bookmarkable") <- FALSE

R/tm_g_association.R

@@ -138,7 +138,8 @@ tm_g_association <- function(label = "Association",
                              pre_output = NULL,
                              post_output = NULL,
                              ggplot2_args = teal.widgets::ggplot2_args(),
-                             decorators = NULL) {
+                             transformators = list(),
+                             decorators = list()) {
   message("Initializing tm_g_association")
 
   # Normalize the parameters
@@ -176,7 +177,7 @@ tm_g_association <- function(label = "Association",
   checkmate::assert_subset(names(ggplot2_args), c("default", plot_choices))
 
   decorators <- normalize_decorators(decorators)
-  assert_decorators(decorators, null.ok = TRUE, "plot")
+  assert_decorators(decorators, "plot")
   # End of assertions
 
   # Make UI args
@@ -196,6 +197,7 @@ tm_g_association <- function(label = "Association",
       data_extract_list,
       list(plot_height = plot_height, plot_width = plot_width, ggplot2_args = ggplot2_args, decorators = decorators)
     ),
+    transformators = transformators,
     datanames = teal.transform::get_extract_datanames(data_extract_list)
   )
   attr(ans, "teal_bookmarkable") <- TRUE

R/tm_g_bivariate.R

@@ -195,7 +195,8 @@ tm_g_bivariate <- function(label = "Bivariate Plots",
                            ggplot2_args = teal.widgets::ggplot2_args(),
                            pre_output = NULL,
                            post_output = NULL,
-                           decorators = NULL) {
+                           transformators = list(),
+                           decorators = list()) {
   message("Initializing tm_g_bivariate")
 
   # Normalize the parameters
@@ -277,7 +278,7 @@ tm_g_bivariate <- function(label = "Bivariate Plots",
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
 
   decorators <- normalize_decorators(decorators)
-  assert_decorators(decorators, null.ok = TRUE, "plot")
+  assert_decorators(decorators, "plot")
   # End of assertions
 
   # Make UI args
@@ -303,6 +304,7 @@ tm_g_bivariate <- function(label = "Bivariate Plots",
       data_extract_list,
       list(plot_height = plot_height, plot_width = plot_width, ggplot2_args = ggplot2_args, decorators = decorators)
     ),
+    transformators = transformators,
     datanames = teal.transform::get_extract_datanames(data_extract_list)
   )
   attr(ans, "teal_bookmarkable") <- TRUE

R/tm_g_distribution.R

@@ -150,7 +150,8 @@ tm_g_distribution <- function(label = "Distribution Module",
                               plot_width = NULL,
                               pre_output = NULL,
                               post_output = NULL,
-                              decorators = NULL) {
+                              transformators = list(),
+                              decorators = list()) {
   message("Initializing tm_g_distribution")
 
   # Normalize the parameters
@@ -194,7 +195,7 @@ tm_g_distribution <- function(label = "Distribution Module",
 
   available_decorators <- c("histogram_plot", "qq_plot", "test_table", "summary_table")
   decorators <- normalize_decorators(decorators)
-  assert_decorators(decorators, null.ok = TRUE, names = available_decorators)
+  assert_decorators(decorators, names = available_decorators)
 
   # End of assertions
 
@@ -221,6 +222,7 @@ tm_g_distribution <- function(label = "Distribution Module",
     ),
     ui = ui_distribution,
     ui_args = args,
+    transformators = transformators,
     datanames = teal.transform::get_extract_datanames(data_extract_list)
   )
   attr(ans, "teal_bookmarkable") <- TRUE

R/tm_g_response.R

@@ -156,7 +156,8 @@ tm_g_response <- function(label = "Response Plot",
                           ggplot2_args = teal.widgets::ggplot2_args(),
                           pre_output = NULL,
                           post_output = NULL,
-                          decorators = NULL) {
+                          transformators = list(),
+                          decorators = list()) {
   message("Initializing tm_g_response")
 
   # Normalize the parameters
@@ -202,7 +203,7 @@ tm_g_response <- function(label = "Response Plot",
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
 
   decorators <- normalize_decorators(decorators)
-  assert_decorators(decorators, null.ok = TRUE, "plot")
+  assert_decorators(decorators, "plot")
   # End of assertions
 
   # Make UI args
@@ -229,6 +230,7 @@ tm_g_response <- function(label = "Response Plot",
         decorators = decorators
       )
     ),
+    transformators = transformators,
     datanames = teal.transform::get_extract_datanames(data_extract_list)
   )
   attr(ans, "teal_bookmarkable") <- TRUE

R/tm_g_scatterplot.R

@@ -239,7 +239,8 @@ tm_g_scatterplot <- function(label = "Scatterplot",
                              post_output = NULL,
                              table_dec = 4,
                              ggplot2_args = teal.widgets::ggplot2_args(),
-                             decorators = NULL) {
+                             transformators = list(),
+                             decorators = list()) {
   message("Initializing tm_g_scatterplot")
 
   # Normalize the parameters
@@ -299,7 +300,7 @@ tm_g_scatterplot <- function(label = "Scatterplot",
   checkmate::assert_class(ggplot2_args, "ggplot2_args")
 
   decorators <- normalize_decorators(decorators)
-  assert_decorators(decorators, null.ok = TRUE, "plot")
+  assert_decorators(decorators, "plot")
 
   # End of assertions
 
@@ -330,6 +331,7 @@ tm_g_scatterplot <- function(label = "Scatterplot",
         decorators = decorators
       )
     ),
+    transformators = transformators,
     datanames = teal.transform::get_extract_datanames(data_extract_list)
   )
   attr(ans, "teal_bookmarkable") <- TRUE

R/tm_g_scatterplotmatrix.R

@@ -177,7 +177,8 @@ tm_g_scatterplotmatrix <- function(label = "Scatterplot Matrix",
                                    plot_width = NULL,
                                    pre_output = NULL,
                                    post_output = NULL,
-                                   decorators = NULL) {
+                                   transformators = list(),
+                                   decorators = list()) {
   message("Initializing tm_g_scatterplotmatrix")
 
   # Normalize the parameters
@@ -199,7 +200,7 @@ tm_g_scatterplotmatrix <- function(label = "Scatterplot Matrix",
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
 
   decorators <- normalize_decorators(decorators)
-  assert_decorators(decorators, null.ok = TRUE, "plot")
+  assert_decorators(decorators, "plot")
   # End of assertions
 
   # Make UI args
@@ -216,6 +217,7 @@ tm_g_scatterplotmatrix <- function(label = "Scatterplot Matrix",
       plot_width = plot_width,
       decorators = decorators
     ),
+    transformators = transformators,
     datanames = teal.transform::get_extract_datanames(variables)
   )
   attr(ans, "teal_bookmarkable") <- TRUE

R/tm_missing_data.R

@@ -118,7 +118,8 @@ tm_missing_data <- function(label = "Missing data",
                             ),
                             pre_output = NULL,
                             post_output = NULL,
-                            decorators = NULL) {
+                            transformators = list(),
+                            decorators = list()) {
   message("Initializing tm_missing_data")
 
   # Normalize the parameters
@@ -148,7 +149,7 @@ tm_missing_data <- function(label = "Missing data",
 
   available_decorators <- c("summary_plot", "combination_plot", "by_subject_plot", "summary_table")
   decorators <- normalize_decorators(decorators)
-  assert_decorators(decorators, null.ok = TRUE, names = available_decorators)
+  assert_decorators(decorators, names = available_decorators)
   # End of assertions
 
   ans <- module(
@@ -164,6 +165,7 @@ tm_missing_data <- function(label = "Missing data",
       decorators = decorators
     ),
     ui = ui_page_missing_data,
+    transformators = transformators,
     ui_args = list(pre_output = pre_output, post_output = post_output)
   )
   attr(ans, "teal_bookmarkable") <- TRUE

R/tm_outliers.R

@@ -157,7 +157,8 @@ tm_outliers <- function(label = "Outliers Module",
                         plot_width = NULL,
                         pre_output = NULL,
                         post_output = NULL,
-                        decorators = NULL) {
+                        transformators = list(),
+                        decorators = list()) {
   message("Initializing tm_outliers")
 
   # Normalize the parameters
@@ -197,7 +198,7 @@ tm_outliers <- function(label = "Outliers Module",
 
   available_decorators <- c("box_plot", "density_plot", "cumulative_plot", "table")
   decorators <- normalize_decorators(decorators)
-  assert_decorators(decorators, null.ok = TRUE, names = available_decorators)
+  assert_decorators(decorators, names = available_decorators)
   # End of assertions
 
   # Make UI args
@@ -221,6 +222,7 @@ tm_outliers <- function(label = "Outliers Module",
     ),
     ui = ui_outliers,
     ui_args = args,
+    transformators = transformators,
     datanames = teal.transform::get_extract_datanames(data_extract_list)
   )
   attr(ans, "teal_bookmarkable") <- TRUE

R/tm_t_crosstable.R

@@ -143,7 +143,8 @@ tm_t_crosstable <- function(label = "Cross Table",
                             pre_output = NULL,
                             post_output = NULL,
                             basic_table_args = teal.widgets::basic_table_args(),
-                            decorators = NULL) {
+                            transformators = list(),
+                            decorators = list()) {
   message("Initializing tm_t_crosstable")
 
   # Normalize the parameters
@@ -164,7 +165,7 @@ tm_t_crosstable <- function(label = "Cross Table",
   checkmate::assert_class(basic_table_args, classes = "basic_table_args")
 
   decorators <- normalize_decorators(decorators)
-  assert_decorators(decorators, null.ok = TRUE, "plot")
+  assert_decorators(decorators, "plot")
   # End of assertions
 
   # Make UI args
@@ -184,6 +185,7 @@ tm_t_crosstable <- function(label = "Cross Table",
     ui = ui_t_crosstable,
     ui_args = ui_args,
     server_args = server_args,
+    transformators = transformators,
     datanames = teal.transform::get_extract_datanames(list(x = x, y = y))
   )
   attr(ans, "teal_bookmarkable") <- TRUE

R/utils.R

@@ -34,8 +34,8 @@
 #' - When the length of `size` is three: the plot points size are dynamically adjusted based on
 #' vector of `value`, `min`, and `max`.
 #' @param decorators `r lifecycle::badge("experimental")`
-#' (`list` of `teal_transform_module`, named `list` of `teal_transform_module` or `NULL`) optional,
-#' if not `NULL`, decorator for tables or plots included in the module.
+#' (`list` of `teal_transform_module`, named `list` of `teal_transform_module`) optional,
+#' decorator for tables or plots included in the module output reported.
 #' When a named list of `teal_transform_module`, the decorators are applied to the respective output objects.
 #'
 #' Otherwise, the decorators are applied to all objects, which is equivalent as using the name `default`.
@@ -342,14 +342,9 @@ ui_decorate_teal_data <- function(id, decorators, ...) {
 
 #' Internal function to check if decorators is a valid object
 #' @noRd
-check_decorators <- function(x, names = NULL, null.ok = FALSE) { # nolint: object_name.
-  checkmate::qassert(null.ok, "B1")
+check_decorators <- function(x, names = NULL) { # nolint: object_name.
 
-  check_message <- checkmate::check_list(
-    x,
-    null.ok = null.ok,
-    names = "named"
-  )
+  check_message <- checkmate::check_list(x, names = "named")
 
   if (!is.null(names)) {
     check_message <- if (isTRUE(check_message)) {
@@ -373,7 +368,6 @@ check_decorators <- function(x, names = NULL, null.ok = FALSE) { # nolint: objec
     x,
     checkmate::test_list,
     types = "teal_transform_module",
-    null.ok = TRUE,
     FUN.VALUE = logical(1L)
   )
 
@@ -411,7 +405,7 @@ select_decorators <- function(decorators, scope) {
 #' @return A named list of lists with `teal_transform_module` objects.
 #' @keywords internal
 normalize_decorators <- function(decorators) {
-  if (checkmate::test_list(decorators, "teal_transform_module", null.ok = TRUE)) {
+  if (checkmate::test_list(decorators, "teal_transform_module")) {
     if (checkmate::test_names(names(decorators))) {
       lapply(decorators, list)
     } else {