From d29d166ca0b77b7f0e6871a08a56a2b3f830cfc7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?= <211358+averissimo@users.noreply.github.com> Date: Tue, 10 Dec 2024 13:04:13 +0000 Subject: [PATCH] Adds decorators to `tm_t_shift_by_grade` (#1285) Part of https://github.com/insightsengineering/teal/issues/1371
Working example ```r pkgload::load_all("../teal.modules.clinical", export_all = FALSE) # Example below insert_rrow_decorator <- function(default_caption = "I am a good new row", .var_to_replace = "table") { teal_transform_module( label = "New row", ui = function(id) shiny::textInput(shiny::NS(id, "new_row"), "New row", value = default_caption), server = make_teal_transform_server( substitute({ .var_to_replace <- rtables::insert_rrow(.var_to_replace, rtables::rrow(new_row)) }, env = list(.var_to_replace = as.name(.var_to_replace))) ) ) } data <- teal_data() data <- within(data, { ADSL <- tmc_ex_adsl ADLB <- tmc_ex_adlb }) join_keys(data) <- default_cdisc_join_keys[names(data)] ADSL <- data[["ADSL"]] ADLB <- data[["ADLB"]] init( data = data, modules = modules( tm_t_shift_by_grade( label = "Grade Laboratory Abnormality Table", dataname = "ADLB", arm_var = choices_selected( choices = variable_choices(ADSL, subset = c("ARM", "ARMCD")), selected = "ARM" ), paramcd = choices_selected( choices = value_choices(ADLB, "PARAMCD", "PARAM"), selected = "ALT" ), worst_flag_var = choices_selected( choices = variable_choices(ADLB, subset = c("WGRLOVFL", "WGRLOFL", "WGRHIVFL", "WGRHIFL")), selected = c("WGRLOVFL") ), worst_flag_indicator = choices_selected( value_choices(ADLB, "WGRLOVFL"), selected = "Y", fixed = TRUE ), anl_toxgrade_var = choices_selected( choices = variable_choices(ADLB, subset = c("ATOXGR")), selected = c("ATOXGR"), fixed = TRUE ), base_toxgrade_var = choices_selected( choices = variable_choices(ADLB, subset = c("BTOXGR")), selected = c("BTOXGR"), fixed = TRUE ), add_total = FALSE, decorators = list(insert_rrow_decorator()) ) ), filter = teal_slices(teal_slice("ADSL", "SAFFL", selected = "Y")) ) |> shiny::runApp() ```
--------- Co-authored-by: Marcin <133694481+m7pr@users.noreply.github.com> --- R/tm_t_shift_by_grade.R | 39 ++++++++++++++++++++++++++++++-------- man/tm_t_shift_by_grade.Rd | 24 ++++++++++++++++++++++- 2 files changed, 54 insertions(+), 9 deletions(-) diff --git a/R/tm_t_shift_by_grade.R b/R/tm_t_shift_by_grade.R index f45ec5372..97256f3f6 100644 --- a/R/tm_t_shift_by_grade.R +++ b/R/tm_t_shift_by_grade.R @@ -449,9 +449,8 @@ template_shift_by_grade <- function(parentname, y$table <- substitute( expr = { - result <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = parent) %>% + table <- rtables::build_table(lyt = lyt, df = anl, alt_counts_df = parent) %>% rtables::prune_table() - result }, env = list(parent = as.name(parentname)) ) @@ -472,6 +471,14 @@ template_shift_by_grade <- function(parentname, #' #' @inherit module_arguments return seealso #' +#' @section Decorating Module: +#' +#' This module generates the following objects, which can be modified in place using decorators: +#' - `table` (`TableTree` - output of `rtables::build_table`) +#' +#' For additional details and examples of decorators, refer to the vignette +#' `vignette("decorate-modules-output", package = "teal")` or the [`teal_transform_module()`] documentation. +#' #' @examplesShinylive #' library(teal.modules.clinical) #' interactive <- function() TRUE @@ -572,7 +579,8 @@ tm_t_shift_by_grade <- function(label, post_output = NULL, na_level = default_na_str(), code_missing_baseline = FALSE, - basic_table_args = teal.widgets::basic_table_args()) { + basic_table_args = teal.widgets::basic_table_args(), + decorators = NULL) { message("Initializing tm_t_shift_by_grade") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -593,6 +601,8 @@ tm_t_shift_by_grade <- function(label, checkmate::assert_class(pre_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(post_output, classes = "shiny.tag", null.ok = TRUE) checkmate::assert_class(basic_table_args, "basic_table_args") + decorators <- normalize_decorators(decorators) + assert_decorators(decorators, null.ok = TRUE, "table") args <- as.list(environment()) @@ -619,7 +629,8 @@ tm_t_shift_by_grade <- function(label, label = label, total_label = total_label, na_level = na_level, - basic_table_args = basic_table_args + basic_table_args = basic_table_args, + decorators = decorators ) ), datanames = teal.transform::get_extract_datanames(data_extract_list) @@ -704,6 +715,7 @@ ui_t_shift_by_grade <- function(id, ...) { ) ) ), + ui_decorate_teal_data(ns("decorator"), decorators = select_decorators(a$decorators, "table")), teal.widgets::panel_group( teal.widgets::panel_item( "Additional Variables Info", @@ -751,7 +763,8 @@ srv_t_shift_by_grade <- function(id, drop_arm_levels, na_level, label, - basic_table_args) { + basic_table_args, + decorators) { with_reporter <- !missing(reporter) && inherits(reporter, "Reporter") with_filter <- !missing(filter_panel_api) && inherits(filter_panel_api, "FilterPanelAPI") checkmate::assert_class(data, "reactive") @@ -840,6 +853,7 @@ srv_t_shift_by_grade <- function(id, ) }) + # Generate r code for the analysis. all_q <- reactive({ validate_checks() @@ -865,8 +879,16 @@ srv_t_shift_by_grade <- function(id, teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls))) }) + # Decoration of table output. + decorated_table_q <- srv_decorate_teal_data( + id = "decorator", + data = all_q, + decorators = select_decorators(decorators, "table"), + expr = table + ) + # Outputs to render. - table_r <- reactive(all_q()[["result"]]) + table_r <- reactive(decorated_table_q()[["table"]]) teal.widgets::table_with_settings_srv( id = "table", @@ -874,9 +896,10 @@ srv_t_shift_by_grade <- function(id, ) # Render R code. + source_code_r <- reactive(teal.code::get_code(req(decorated_table_q()))) teal.widgets::verbatim_popup_srv( id = "rcode", - verbatim_content = reactive(teal.code::get_code(all_q())), + verbatim_content = source_code_r, title = label ) @@ -895,7 +918,7 @@ srv_t_shift_by_grade <- function(id, card$append_text("Comment", "header3") card$append_text(comment) } - card$append_src(teal.code::get_code(all_q())) + card$append_src(source_code_r()) card } teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun) diff --git a/man/tm_t_shift_by_grade.Rd b/man/tm_t_shift_by_grade.Rd index 0af0b42f4..059adb022 100644 --- a/man/tm_t_shift_by_grade.Rd +++ b/man/tm_t_shift_by_grade.Rd @@ -34,7 +34,8 @@ tm_t_shift_by_grade( post_output = NULL, na_level = default_na_str(), code_missing_baseline = FALSE, - basic_table_args = teal.widgets::basic_table_args() + basic_table_args = teal.widgets::basic_table_args(), + decorators = NULL ) } \arguments{ @@ -97,6 +98,15 @@ default \code{na_level} to apply in all modules, run \code{set_default_na_str("n with settings for the module table. The argument is merged with option \code{teal.basic_table_args} and with default module arguments (hard coded in the module body). For more details, see the vignette: \code{vignette("custom-basic-table-arguments", package = "teal.widgets")}.} + +\item{decorators}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}} +" (\code{list} of \code{teal_transform_module}, named \code{list} of \code{teal_transform_module} or" \code{NULL}) optional, +if not \code{NULL}, decorator for tables or plots included in the module. +When a named list of \code{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 \code{default}. + +See section "Decorating Module" below for more details.} } \value{ a \code{teal_module} object. @@ -104,6 +114,18 @@ a \code{teal_module} object. \description{ This module produces a summary table of worst grades per subject by visit and parameter. } +\section{Decorating Module}{ + + +This module generates the following objects, which can be modified in place using decorators: +\itemize{ +\item \code{table} (\code{TableTree} - output of \code{rtables::build_table}) +} + +For additional details and examples of decorators, refer to the vignette +\code{vignette("decorate-modules-output", package = "teal")} or the \code{\link[=teal_transform_module]{teal_transform_module()}} documentation. +} + \examples{ data <- teal_data() data <- within(data, {