From 015a9641edb1e0192b0b6388df54bb55b7cf4bf2 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 13:00:52 +0000 Subject: [PATCH] Adds decorators to `tm_t_smq` (#1292) 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 ADAE <- tmc_ex_adae .names_baskets <- grep("^(SMQ|CQ).*NAM$", names(ADAE), value = TRUE) .names_scopes <- grep("^SMQ.*SC$", names(ADAE), value = TRUE) .cs_baskets <- choices_selected( choices = variable_choices(ADAE, subset = .names_baskets), selected = .names_baskets ) .cs_scopes <- choices_selected( choices = variable_choices(ADAE, subset = .names_scopes), selected = .names_scopes, fixed = TRUE ) }) join_keys(data) <- default_cdisc_join_keys[names(data)] app <- init( data = data, modules = modules( tm_t_smq( label = "Adverse Events by SMQ Table", dataname = "ADAE", arm_var = choices_selected( choices = variable_choices(data[["ADSL"]], subset = c("ARM", "SEX")), selected = "ARM" ), add_total = FALSE, baskets = data[[".cs_baskets"]], scopes = data[[".cs_scopes"]], llt = choices_selected( choices = variable_choices(data[["ADAE"]], subset = c("AEDECOD")), selected = "AEDECOD" ), decorators = list(insert_rrow_decorator()) ) ) ) |> shiny::runApp() ```
--------- Co-authored-by: Marcin <133694481+m7pr@users.noreply.github.com> --- R/tm_t_smq.R | 40 +++++++++++++++++++++++++++++++--------- man/tm_t_smq.Rd | 24 +++++++++++++++++++++++- 2 files changed, 54 insertions(+), 10 deletions(-) diff --git a/R/tm_t_smq.R b/R/tm_t_smq.R index e1081cdec..b79251aca 100644 --- a/R/tm_t_smq.R +++ b/R/tm_t_smq.R @@ -290,8 +290,7 @@ template_smq <- function(dataname, all_zero <- function(tr) { !inherits(tr, "ContentRow") && rtables::all_zero_or_na(tr) } - pruned_and_sorted_result <- sorted_result %>% rtables::trim_rows(criteria = all_zero) - pruned_and_sorted_result + table <- sorted_result %>% rtables::trim_rows(criteria = all_zero) } ) @@ -316,6 +315,14 @@ template_smq <- function(dataname, #' #' @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 @@ -391,7 +398,8 @@ tm_t_smq <- function(label, scopes, pre_output = NULL, post_output = NULL, - basic_table_args = teal.widgets::basic_table_args()) { + basic_table_args = teal.widgets::basic_table_args(), + decorators = NULL) { message("Initializing tm_t_smq") checkmate::assert_string(label) checkmate::assert_string(dataname) @@ -408,6 +416,8 @@ tm_t_smq <- 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()) @@ -432,7 +442,8 @@ tm_t_smq <- function(label, na_level = na_level, label = label, total_label = total_label, - basic_table_args = basic_table_args + basic_table_args = basic_table_args, + decorators = decorators ) ), datanames = teal.transform::get_extract_datanames(data_extract_list) @@ -444,7 +455,6 @@ ui_t_smq <- function(id, ...) { ns <- NS(id) a <- list(...) # module args - is_single_dataset_value <- teal.transform::is_single_dataset( a$arm_var, a$id_var, @@ -482,6 +492,7 @@ ui_t_smq <- function(id, ...) { data_extract_spec = a$baskets, is_single_dataset = is_single_dataset_value ), + ui_decorate_teal_data(ns("decorator"), decorators = select_decorators(a$decorators, "table")), teal.widgets::panel_group( teal.widgets::panel_item( "Additional Variables Info", @@ -540,7 +551,8 @@ srv_t_smq <- function(id, na_level, label, total_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") @@ -621,6 +633,7 @@ srv_t_smq <- function(id, ) }) + # Generate r code for the analysis. all_q <- reactive({ validate_checks() @@ -642,8 +655,16 @@ srv_t_smq <- function(id, teal.code::eval_code(merged$anl_q(), as.expression(unlist(my_calls))) }) + # Decoration of table output. + decorated_table_q <- srv_decorate_teal_data( + id = "decorator", + data = all_q, + decorators = select_decorators(decorators, "table"), + expr = table + ) + # Outputs to render. - table_r <- reactive(all_q()[["pruned_and_sorted_result"]]) + table_r <- reactive(decorated_table_q()[["table"]]) teal.widgets::table_with_settings_srv( id = "table", @@ -651,9 +672,10 @@ srv_t_smq <- function(id, ) # Render R code. + source_code_r <- reactive(teal.code::get_code(req(decorated_table_q()))) teal.widgets::verbatim_popup_srv( id = "rcode", - verbatim_content = reactive(teal.code::get_code(all_q())), + verbatim_content = source_code_r, title = label ) @@ -672,7 +694,7 @@ srv_t_smq <- function(id, card$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_smq.Rd b/man/tm_t_smq.Rd index cd211d8ed..5169323c1 100644 --- a/man/tm_t_smq.Rd +++ b/man/tm_t_smq.Rd @@ -23,7 +23,8 @@ tm_t_smq( scopes, pre_output = NULL, post_output = NULL, - basic_table_args = teal.widgets::basic_table_args() + basic_table_args = teal.widgets::basic_table_args(), + decorators = NULL ) } \arguments{ @@ -82,6 +83,15 @@ For example the \code{\link[shiny:helpText]{shiny::helpText()}} elements are use 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. @@ -89,6 +99,18 @@ a \code{teal_module} object. \description{ This module produces an adverse events table by Standardized MedDRA Query. } +\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, {