1441 Introduce transformators parameter in modules (#293)

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>

R/tm_g_ae_oview.R

@@ -6,6 +6,7 @@
 #' Display the `AE` overview plot as a shiny module
 #'
 #' @inheritParams teal.widgets::standard_layout
+#' @inheritParams teal::module
 #' @inheritParams argument_convention
 #' @param flag_var_anl ([`teal.transform::choices_selected`])
 #'   `choices_selected` object with variables used to count adverse event
@@ -77,7 +78,8 @@ tm_g_ae_oview <- function(label,
                           flag_var_anl,
                           fontsize = c(5, 3, 7),
                           plot_height = c(600L, 200L, 2000L),
-                          plot_width = NULL) {
+                          plot_width = NULL,
+                          transformators = list()) {
   message("Initializing tm_g_ae_oview")
   checkmate::assert_class(arm_var, classes = "choices_selected")
   checkmate::assert_class(flag_var_anl, classes = "choices_selected")
@@ -114,6 +116,7 @@ tm_g_ae_oview <- function(label,
     ),
     ui = ui_g_ae_oview,
     ui_args = args,
+    transformators = transformators,
     datanames = c("ADSL", dataname)
   )
 }

R/tm_g_ae_sub.R

@@ -6,6 +6,7 @@
 #' Display the `AE` by subgroups plot as a teal module
 #'
 #' @inheritParams teal.widgets::standard_layout
+#' @inheritParams teal::module
 #' @inheritParams argument_convention
 #' @param group_var (`choices_selected`) subgroups variables. See [teal.transform::choices_selected()] for details.
 #'
@@ -54,7 +55,8 @@ tm_g_ae_sub <- function(label,
                         group_var,
                         plot_height = c(600L, 200L, 2000L),
                         plot_width = NULL,
-                        fontsize = c(5, 3, 7)) {
+                        fontsize = c(5, 3, 7),
+                        transformators = list()) {
   message("Initializing tm_g_ae_sub")
   checkmate::assert_class(arm_var, classes = "choices_selected")
   checkmate::assert_class(group_var, classes = "choices_selected")
@@ -90,6 +92,7 @@ tm_g_ae_sub <- function(label,
       group_var = group_var,
       fontsize = fontsize
     ),
+    transformators = transformators,
     datanames = c("ADSL", dataname)
   )
 }

R/tm_g_butterfly.R

@@ -6,6 +6,7 @@
 #' Display butterfly plot as a shiny module
 #'
 #' @inheritParams teal.widgets::standard_layout
+#' @inheritParams teal::module
 #' @inheritParams argument_convention
 #' @param filter_var (`choices_selected`) variable name of data filter, please see details regarding
 #'   expected values, default is`NULL`.`choices`
@@ -118,7 +119,8 @@ tm_g_butterfly <- function(label,
                            plot_height = c(600L, 200L, 2000L),
                            plot_width = NULL,
                            pre_output = NULL,
-                           post_output = NULL) {
+                           post_output = NULL,
+                           transformators = list()) {
   message("Initializing tm_g_butterfly")
   checkmate::assert_string(label)
   checkmate::assert_string(dataname)
@@ -150,7 +152,8 @@ tm_g_butterfly <- function(label,
     server = srv_g_butterfly,
     server_args = list(dataname = dataname, label = label, plot_height = plot_height, plot_width = plot_width),
     ui = ui_g_butterfly,
-    ui_args = args
+    ui_args = args,
+    transformators = transformators
   )
 }
 

R/tm_g_events_term_id.R

@@ -6,6 +6,7 @@
 #' Display Events by Term plot as a shiny module
 #'
 #' @inheritParams teal.widgets::standard_layout
+#' @inheritParams teal::module
 #' @inheritParams argument_convention
 #' @param term_var [teal.transform::choices_selected] object with all available choices
 #' and pre-selected option names that can be used to specify the term for events
@@ -57,7 +58,8 @@ tm_g_events_term_id <- function(label,
                                 arm_var,
                                 fontsize = c(5, 3, 7),
                                 plot_height = c(600L, 200L, 2000L),
-                                plot_width = NULL) {
+                                plot_width = NULL,
+                                transformators = list()) {
   message("Initializing tm_g_events_term_id")
   checkmate::assert_string(label)
   checkmate::assert_class(term_var, classes = "choices_selected")
@@ -90,6 +92,7 @@ tm_g_events_term_id <- function(label,
     server_args = list(label = label, dataname = dataname, plot_height = plot_height, plot_width = plot_width),
     ui = ui_g_events_term_id,
     ui_args = args,
+    transformators = transformators,
     datanames = c("ADSL", dataname)
   )
 }

R/tm_g_heat_bygrade.R

@@ -6,6 +6,7 @@
 #' Display the heatmap by grade as a shiny module
 #'
 #' @inheritParams teal.widgets::standard_layout
+#' @inheritParams teal::module
 #' @inheritParams argument_convention
 #' @param sl_dataname (`character`) subject level dataset name,
 #' needs to be available in the list passed to the `data`
@@ -129,7 +130,8 @@ tm_g_heat_bygrade <- function(label,
                               conmed_var = NULL,
                               fontsize = c(5, 3, 7),
                               plot_height = c(600L, 200L, 2000L),
-                              plot_width = NULL) {
+                              plot_width = NULL,
+                              transformators = list()) {
   message("Initializing tm_g_heat_bygrade")
   args <- as.list(environment())
 
@@ -178,6 +180,7 @@ tm_g_heat_bygrade <- function(label,
     ),
     ui = ui_g_heatmap_bygrade,
     ui_args = args,
+    transformators = transformators,
     datanames = "all"
   )
 }

R/tm_g_patient_profile.R

@@ -6,6 +6,7 @@
 #' Display patient profile plot as a shiny module
 #'
 #' @inheritParams teal.widgets::standard_layout
+#' @inheritParams teal::module
 #' @inheritParams argument_convention
 #' @param patient_id (`choices_seleced`) unique subject ID variable
 #' @param sl_dataname (`character`) subject level dataset name,
@@ -151,7 +152,8 @@ tm_g_patient_profile <- function(label = "Patient Profile Plot",
                                  plot_height = c(1200L, 400L, 5000L),
                                  plot_width = NULL,
                                  pre_output = NULL,
-                                 post_output = NULL) {
+                                 post_output = NULL,
+                                 transformators = list()) {
   args <- as.list(environment())
   checkmate::assert_string(label)
   checkmate::assert_string(sl_dataname)
@@ -201,6 +203,7 @@ tm_g_patient_profile <- function(label = "Patient Profile Plot",
       plot_height = plot_height,
       plot_width = plot_width
     ),
+    transformators = transformators,
     datanames = "all"
   )
 }

R/tm_g_spiderplot.R

@@ -6,6 +6,7 @@
 #' Display spider plot as a shiny module
 #'
 #' @inheritParams teal.widgets::standard_layout
+#' @inheritParams teal::module
 #' @inheritParams argument_convention
 #' @param x_var x-axis variables
 #' @param y_var y-axis variables
@@ -93,7 +94,8 @@ tm_g_spiderplot <- function(label,
                             plot_height = c(600L, 200L, 2000L),
                             plot_width = NULL,
                             pre_output = NULL,
-                            post_output = NULL) {
+                            post_output = NULL,
+                            transformators = list()) {
   message("Initializing tm_g_spiderplot")
   checkmate::assert_class(paramcd, classes = "choices_selected")
   checkmate::assert_class(x_var, classes = "choices_selected")
@@ -130,7 +132,8 @@ tm_g_spiderplot <- function(label,
       plot_width = plot_width
     ),
     ui = ui_g_spider,
-    ui_args = args
+    ui_args = args,
+    transformators = transformators
   )
 }
 

R/tm_g_swimlane.R

@@ -6,6 +6,7 @@
 #' This is teal module that generates a `swimlane` plot (bar plot with markers) for `ADaM` data
 #'
 #' @inheritParams teal.widgets::standard_layout
+#' @inheritParams teal::module
 #' @inheritParams argument_convention
 #' @param dataname analysis data used for plotting, needs to be available in the list passed to the `data`
 #' argument of [teal::init()]. If no markers are to be plotted in the module, `"ADSL"` should be
@@ -120,7 +121,8 @@ tm_g_swimlane <- function(label,
                           plot_width = NULL,
                           pre_output = NULL,
                           post_output = NULL,
-                          x_label = "Time from First Treatment (Day)") {
+                          x_label = "Time from First Treatment (Day)",
+                          transformators = list()) {
   message("Initializing tm_g_swimlane")
   args <- as.list(environment())
 
@@ -165,6 +167,7 @@ tm_g_swimlane <- function(label,
       plot_width = plot_width,
       x_label = x_label
     ),
+    transformators = transformators,
     datanames = c("ADSL", dataname)
   )
 }

R/tm_g_waterfall.R

@@ -6,6 +6,7 @@
 #' This is teal module that generates a waterfall plot for `ADaM` data
 #'
 #' @inheritParams teal.widgets::standard_layout
+#' @inheritParams teal::module
 #' @inheritParams argument_convention
 #' @param dataname_tr tumor burden analysis data used in teal module to plot as bar height, needs to
 #' be available in the list passed to the `data` argument of [teal::init()]
@@ -102,7 +103,8 @@ tm_g_waterfall <- function(label,
                            plot_height = c(1200L, 400L, 5000L),
                            plot_width = NULL,
                            pre_output = NULL,
-                           post_output = NULL) {
+                           post_output = NULL,
+                           transformators = list()) {
   message("Initializing tm_g_waterfall")
   checkmate::assert_string(label)
   checkmate::assert_string(dataname_tr)
@@ -145,6 +147,7 @@ tm_g_waterfall <- function(label,
       plot_height = plot_height,
       plot_width = plot_width
     ),
+    transformators = transformators,
     datanames = "all"
   )
 }