Remove "default" decoration and use the same way of decoration in all modules

R/tm_a_pca.R

@@ -25,20 +25,18 @@
 #' - `biplot` (`ggplot2`)
 #' - `eigenvector_plot` (`ggplot2`)
 #'
-#' Decorators can be applied to all outputs or only to specific objects using a
-#' named list of `teal_transform_module` objects.
-#' The `"default"` name is reserved for decorators that are applied to all outputs.
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
 #' See code snippet below:
 #'
 #' ```
 #' tm_a_pca(
 #'    ..., # arguments for module
 #'    decorators = list(
-#'      default = list(teal_transform_module(...)), # applied to all outputs
-#'      elbow_plot = list(teal_transform_module(...)), # applied only to `elbow_plot` output
-#'      circle_plot = list(teal_transform_module(...)) # applied only to `circle_plot` output
-#'      biplot = list(teal_transform_module(...)) # applied only to `biplot` output
-#'      eigenvector_plot = list(teal_transform_module(...)) # applied only to `eigenvector_plot` output
+#'      elbow_plot = teal_transform_module(...), # applied to the `elbow_plot` output
+#'      circle_plot = teal_transform_module(...), # applied to the `circle_plot` output
+#'      biplot = teal_transform_module(...), # applied to the `biplot` output
+#'      eigenvector_plot = teal_transform_module(...) # applied to the `eigenvector_plot` output
 #'    )
 #' )
 #' ```
@@ -186,9 +184,7 @@ tm_a_pca <- function(label = "Principal Component Analysis",
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
 
   available_decorators <- c("elbow_plot", "circle_plot", "biplot", "eigenvector_plot")
-  decorators <- normalize_decorators(decorators)
   assert_decorators(decorators, available_decorators)
-  # End of assertions
 
   # Make UI args
   args <- as.list(environment())

R/tm_a_regression.R

@@ -48,6 +48,19 @@
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `plot` (`ggplot2`)
 #'
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
+#' See code snippet below:
+#'
+#' ```
+#' tm_a_regression(
+#'    ..., # arguments for module
+#'    decorators = list(
+#'      plot = teal_transform_module(...) # applied to the `plot` output
+#'    )
+#' )
+#' ```
+#'
 #' For additional details and examples of decorators, refer to the vignette
 #' `vignette("decorate-modules-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
@@ -225,7 +238,6 @@ tm_a_regression <- function(label = "Regression Analysis",
       .var.name = "label_segment_threshold"
     )
   }
-  decorators <- normalize_decorators(decorators)
   assert_decorators(decorators, "plot")
   # End of assertions
 

R/tm_g_association.R

@@ -29,6 +29,19 @@
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `plot` (`grob` created with [ggplot2::ggplotGrob()])
 #'
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
+#' See code snippet below:
+#'
+#' ```
+#' tm_g_association(
+#'    ..., # arguments for module
+#'    decorators = list(
+#'      plot = teal_transform_module(...) # applied to the `plot` output
+#'    )
+#' )
+#' ```
+#'
 #' For additional details and examples of decorators, refer to the vignette
 #' `vignette("decorate-modules-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
@@ -176,7 +189,6 @@ tm_g_association <- function(label = "Association",
   checkmate::assert_list(ggplot2_args, types = "ggplot2_args")
   checkmate::assert_subset(names(ggplot2_args), c("default", plot_choices))
 
-  decorators <- normalize_decorators(decorators)
   assert_decorators(decorators, "plot")
   # End of assertions
 

R/tm_g_bivariate.R

@@ -51,6 +51,19 @@
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `plot` (`ggplot2`)
 #'
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
+#' See code snippet below:
+#'
+#' ```
+#' tm_g_bivariate(
+#'    ..., # arguments for module
+#'    decorators = list(
+#'      plot = teal_transform_module(...) # applied to the `plot` output
+#'    )
+#' )
+#' ```
+#'
 #' For additional details and examples of decorators, refer to the vignette
 #' `vignette("decorate-modules-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
@@ -277,7 +290,6 @@ tm_g_bivariate <- function(label = "Bivariate Plots",
   checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
 
-  decorators <- normalize_decorators(decorators)
   assert_decorators(decorators, "plot")
   # End of assertions
 

R/tm_g_distribution.R

@@ -34,20 +34,18 @@
 #' - `summary_table` (`listing_df` created with [rlistings::as_listing()])
 #' - `test_table` (`listing_df` created with [rlistings::as_listing()])
 #'
-#' Decorators can be applied to all outputs or only to specific objects using a
-#' named list of `teal_transform_module` objects.
-#' The `"default"` name is reserved for decorators that are applied to all outputs.
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
 #' See code snippet below:
 #'
 #' ```
 #' tm_g_distribution(
 #'    ..., # arguments for module
 #'    decorators = list(
-#'      default = list(teal_transform_module(...)), # applied to all outputs
-#'      histogram_plot = list(teal_transform_module(...)), # applied only to `histogram_plot` output
-#'      qq_plot = list(teal_transform_module(...)) # applied only to `qq_plot` output
-#'      summary_table = list(teal_transform_module(...)) # applied only to `summary_table` output
-#'      test_table = list(teal_transform_module(...)) # applied only to `test_table` output
+#'      histogram_plot = teal_transform_module(...), # applied only to `histogram_plot` output
+#'      qq_plot = teal_transform_module(...), # applied only to `qq_plot` output
+#'      summary_table = teal_transform_module(...), # applied only to `summary_table` output
+#'      test_table = teal_transform_module(...) # applied only to `test_table` output
 #'    )
 #' )
 #' ```
@@ -194,7 +192,6 @@ tm_g_distribution <- function(label = "Distribution Module",
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
 
   available_decorators <- c("histogram_plot", "qq_plot", "test_table", "summary_table")
-  decorators <- normalize_decorators(decorators)
   assert_decorators(decorators, names = available_decorators)
 
   # End of assertions

R/tm_g_response.R

@@ -44,6 +44,19 @@
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `plot` (`ggplot2`)
 #'
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
+#' See code snippet below:
+#'
+#' ```
+#' tm_g_response(
+#'    ..., # arguments for module
+#'    decorators = list(
+#'      plot = teal_transform_module(...) # applied to the `plot` output
+#'    )
+#' )
+#' ```
+#'
 #' For additional details and examples of decorators, refer to the vignette
 #' `vignette("decorate-modules-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
@@ -202,7 +215,6 @@ tm_g_response <- function(label = "Response Plot",
   checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
 
-  decorators <- normalize_decorators(decorators)
   assert_decorators(decorators, "plot")
   # End of assertions
 

R/tm_g_scatterplot.R

@@ -35,6 +35,19 @@
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `plot` (`ggplot2`)
 #'
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
+#' See code snippet below:
+#'
+#' ```
+#' tm_g_scatterplot(
+#'    ..., # arguments for module
+#'    decorators = list(
+#'      plot = teal_transform_module(...) # applied to the `plot` output
+#'    )
+#' )
+#' ```
+#'
 #' For additional details and examples of decorators, refer to the vignette
 #' `vignette("decorate-modules-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
@@ -299,7 +312,6 @@ tm_g_scatterplot <- function(label = "Scatterplot",
   checkmate::assert_scalar(table_dec)
   checkmate::assert_class(ggplot2_args, "ggplot2_args")
 
-  decorators <- normalize_decorators(decorators)
   assert_decorators(decorators, "plot")
 
   # End of assertions

R/tm_g_scatterplotmatrix.R

@@ -23,6 +23,19 @@
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `plot` (`trellis` - output of `lattice::splom`)
 #'
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
+#' See code snippet below:
+#'
+#' ```
+#' tm_g_scatterplotmatrix(
+#'    ..., # arguments for module
+#'    decorators = list(
+#'      plot = teal_transform_module(...) # applied to the `plot` output
+#'    )
+#' )
+#' ```
+#'
 #' For additional details and examples of decorators, refer to the vignette
 #' `vignette("decorate-modules-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
@@ -199,7 +212,6 @@ tm_g_scatterplotmatrix <- function(label = "Scatterplot Matrix",
   checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
 
-  decorators <- normalize_decorators(decorators)
   assert_decorators(decorators, "plot")
   # End of assertions
 

R/tm_missing_data.R

@@ -25,20 +25,18 @@
 #' - `by_subject_plot` (`ggplot2`)
 #' - `table` (`listing_df` created with [rlistings::as_listing()])
 #'
-#' Decorators can be applied to all outputs or only to specific objects using a
-#' named list of `teal_transform_module` objects.
-#' The `"default"` name is reserved for decorators that are applied to all outputs.
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
 #' See code snippet below:
 #'
 #' ```
 #' tm_missing_data(
 #'    ..., # arguments for module
 #'    decorators = list(
-#'      default = list(teal_transform_module(...)), # applied to all outputs
-#'      summary_plot = list(teal_transform_module(...)), # applied only to `summary_plot` output
-#'      combination_plot = list(teal_transform_module(...)) # applied only to `combination_plot` output
-#'      by_subject_plot = list(teal_transform_module(...)) # applied only to `by_subject_plot` output
-#'      table = list(teal_transform_module(...)) # applied only to `table` output
+#'      summary_plot = teal_transform_module(...), # applied only to `summary_plot` output
+#'      combination_plot = teal_transform_module(...), # applied only to `combination_plot` output
+#'      by_subject_plot = teal_transform_module(...), # applied only to `by_subject_plot` output
+#'      table = teal_transform_module(...) # applied only to `table` output
 #'    )
 #' )
 #' ```
@@ -147,8 +145,7 @@ tm_missing_data <- function(label = "Missing data",
   checkmate::assert_multi_class(pre_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
 
-  available_decorators <- c("summary_plot", "combination_plot", "by_subject_plot", "summary_table")
-  decorators <- normalize_decorators(decorators)
+  available_decorators <- c("summary_plot", "combination_plot", "by_subject_plot", "table")
   assert_decorators(decorators, names = available_decorators)
   # End of assertions
 
@@ -446,7 +443,7 @@ encoding_missing_data <- function(id, summary_per_patient = FALSE, ggtheme, data
         selected = "counts",
         inline = TRUE
       ),
-      ui_decorate_teal_data(ns("dec_summary_table"), decorators = select_decorators(decorators, "summary_table"))
+      ui_decorate_teal_data(ns("dec_summary_table"), decorators = select_decorators(decorators, "table"))
     ),
     teal.widgets::panel_item(
       title = "Plot settings",
@@ -1295,7 +1292,7 @@ srv_missing_data <- function(id,
     decorated_summary_table_q <- srv_decorate_teal_data(
       id = "dec_summary_table",
       data = summary_table_q,
-      decorators = select_decorators(decorators, "summary_table"),
+      decorators = select_decorators(decorators, "table"),
       expr = table
     )
 

R/tm_outliers.R

@@ -23,20 +23,18 @@
 #' - `cumulative_plot` (`ggplot2`)
 #' - `table` (`listing_df` created with [rlistings::as_listing()])
 #'
-#' Decorators can be applied to all outputs or only to specific objects using a
-#' named list of `teal_transform_module` objects.
-#' The `"default"` name is reserved for decorators that are applied to all outputs.
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
 #' See code snippet below:
 #'
 #' ```
 #' tm_outliers(
 #'    ..., # arguments for module
 #'    decorators = list(
-#'      default = list(teal_transform_module(...)), # applied to all outputs
-#'      box_plot = list(teal_transform_module(...)), # applied only to `box_plot` output
-#'      density_plot = list(teal_transform_module(...)) # applied only to `density_plot` output
-#'      cumulative_plot = list(teal_transform_module(...)) # applied only to `cumulative_plot` output
-#'      table = list(teal_transform_module(...)) # applied only to `table` output
+#'      box_plot = teal_transform_module(...), # applied only to `box_plot` output
+#'      density_plot = teal_transform_module(...), # applied only to `density_plot` output
+#'      cumulative_plot = teal_transform_module(...), # applied only to `cumulative_plot` output
+#'      table = teal_transform_module(...) # applied only to `table` output
 #'    )
 #' )
 #' ```
@@ -197,7 +195,6 @@ tm_outliers <- function(label = "Outliers Module",
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
 
   available_decorators <- c("box_plot", "density_plot", "cumulative_plot", "table")
-  decorators <- normalize_decorators(decorators)
   assert_decorators(decorators, names = available_decorators)
   # End of assertions
 

R/tm_t_crosstable.R

@@ -30,6 +30,18 @@
 #' This module generates the following objects, which can be modified in place using decorators:
 #' - `table` (`ElementaryTable` - output of `rtables::build_table`)
 #'
+#' A Decorator is applied to the specific output using a named list of `teal_transform_module` objects.
+#' The name of this list corresponds to the name of the output to which the decorator is applied.
+#' See code snippet below:
+#'
+#' ```
+#' tm_t_crosstable(
+#'    ..., # arguments for module
+#'    decorators = list(
+#'      table = teal_transform_module(...) # applied to the `table` output
+#'    )
+#' )
+#' ```
 #' For additional details and examples of decorators, refer to the vignette
 #' `vignette("decorate-modules-output", package = "teal")` or the [`teal::teal_transform_module()`] documentation.
 #'
@@ -164,8 +176,7 @@ tm_t_crosstable <- function(label = "Cross Table",
   checkmate::assert_multi_class(post_output, c("shiny.tag", "shiny.tag.list", "html"), null.ok = TRUE)
   checkmate::assert_class(basic_table_args, classes = "basic_table_args")
 
-  decorators <- normalize_decorators(decorators)
-  assert_decorators(decorators, "plot")
+  assert_decorators(decorators, "table")
   # End of assertions
 
   # Make UI args
@@ -233,7 +244,7 @@ ui_t_crosstable <- function(id, x, y, show_percentage, show_total, pre_output, p
           checkboxInput(ns("show_total"), "Show total column", value = show_total)
         )
       ),
-      ui_decorate_teal_data(ns("decorator"), decorators = select_decorators(args$decorators, "plot"))
+      ui_decorate_teal_data(ns("decorator"), decorators = select_decorators(args$decorators, "table"))
     ),
     forms = tagList(
       teal.widgets::verbatim_popup_ui(ns("rcode"), "Show R code")
@@ -409,7 +420,7 @@ srv_t_crosstable <- function(id, data, reporter, filter_panel_api, label, x, y,
     decorated_output_q <- srv_decorate_teal_data(
       id = "decorator",
       data = output_q,
-      decorators = select_decorators(decorators, "plot"),
+      decorators = select_decorators(decorators, "table"),
       expr = table
     )