introduce decorators for tm_g_pp_adverse_events

[m7pr]

Part of insightsengineering/teal#1371

Working Example

pkgload::load_all("../teal.modules.clinical", export_all = FALSE)

library(nestcolor)
library(dplyr)

data <- teal_data()
data <- within(data, {
  ADAE <- tmc_ex_adae
  ADSL <- tmc_ex_adsl %>%
    filter(USUBJID %in% ADAE$USUBJID)

  ADAE$ASTDY <- structure(
    as.double(ADAE$ASTDY, unit = attr(ADAE$ASTDY, "units", exact = TRUE)),
    label = attr(ADAE$ASTDY, "label", exact = TRUE)
  )
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADAE <- data[["ADAE"]]

caption_decorator <- function(default_caption = "I am a good decorator", .var_to_replace = "plot") {
  teal_transform_module(
    label = "Caption",
    ui = function(id) shiny::textInput(shiny::NS(id, "footnote"), "Footnote", value = default_caption),
    server = make_teal_transform_server(
      substitute({
        .var_to_replace <- .var_to_replace + ggplot2::labs(caption = footnote)
      }, env = list(.var_to_replace = as.name(.var_to_replace)))
    )
  )
}

head_decorator <- function(default_value = 6, .var_to_replace = "object") {
  teal_transform_module(
    label = "Head",
    ui = function(id) shiny::numericInput(shiny::NS(id, "n"), "N rows", value = default_value),
    server = make_teal_transform_server(
      substitute({
        .var_to_replace <- utils::head(.var_to_replace, n = n)
      }, env = list(.var_to_replace = as.name(.var_to_replace)))
    )
  )
}

app <- init(
  data = data,
  modules = modules(
    tm_g_pp_adverse_events(
      label = "Adverse Events",
      dataname = "ADAE",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      aeterm = choices_selected(
        choices = variable_choices(ADAE, "AETERM"),
        selected = "AETERM"
      ),
      tox_grade = choices_selected(
        choices = variable_choices(ADAE, "AETOXGR"),
        selected = "AETOXGR"
      ),
      causality = choices_selected(
        choices = variable_choices(ADAE, "AEREL"),
        selected = "AEREL"
      ),
      outcome = choices_selected(
        choices = variable_choices(ADAE, "AEOUT"),
        selected = "AEOUT"
      ),
      action = choices_selected(
        choices = variable_choices(ADAE, "AEACN"),
        selected = "AEACN"
      ),
      time = choices_selected(
        choices = variable_choices(ADAE, "ASTDY"),
        selected = "ASTDY"
      ),
      decod = NULL,
      decorators = list(plot = caption_decorator('Marcin', 'plot'), table = head_decorator(2, 'table'))
    )
  )
) |> shiny::runApp()

[averissimo]

Example app works great.

Module appears to have a bug

[m7pr]

@averissimo @llrs-roche beware before merging this module, it has a decorator for plot that is dependent on a decorator for a table. If table decorator breaks, you don't see a plot. This is the same scenario as in #1267 (comment)

[llrs-roche]

When running the test I see this on the terminal when I try to create a card:

Error in self$set_content(table) : 
  Assertion on 'content' failed: Must inherit from class 'data.frame'/'rtables'/'TableTree'/'ElementaryTable'/'listing_df', but has class 'NULL'.
Warning in observe() :
  The card could not be added to the report. Have the outputs for the report been created yet? If not please try again when they are ready. Otherwise contact your application developer

Which prevents the shiny app to generate the card.

I also left two minor comments