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Adds decorators to tm_t_shift_by_arm_by_worst (#1286)
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Part of insightsengineering/teal#1371

<details>
<summary>Working example</summary>

```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
  ADEG <- tmc_ex_adeg
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADEG <- data[["ADEG"]]

init(
  data = data,
  modules = modules(
    tm_t_shift_by_arm_by_worst(
      label = "Shift by Arm Table",
      dataname = "ADEG",
      arm_var = choices_selected(
        variable_choices(ADSL, subset = c("ARM", "ARMCD")),
        selected = "ARM"
      ),
      paramcd = choices_selected(
        value_choices(ADEG, "PARAMCD"),
        selected = "ECGINTP"
      ),
      worst_flag_var = choices_selected(
        variable_choices(ADEG, c("WORS02FL", "WORS01FL")),
        selected = "WORS02FL"
      ),
      worst_flag = choices_selected(
        value_choices(ADEG, "WORS02FL"),
        selected = "Y",
        fixed = TRUE
      ),
      aval_var = choices_selected(
        variable_choices(ADEG, c("AVALC", "ANRIND")),
        selected = "AVALC"
      ),
      baseline_var = choices_selected(
        variable_choices(ADEG, c("BASEC", "BNRIND")),
        selected = "BASEC"
      ),
      useNA = "ifany",
      decorators = list(insert_rrow_decorator())
    )
  )
) |> shiny::runApp()
```

</details>

---------

Co-authored-by: Marcin <[email protected]>
  • Loading branch information
averissimo and m7pr authored Dec 10, 2024
1 parent 772c14b commit 582ceb3
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Showing 2 changed files with 55 additions and 11 deletions.
42 changes: 32 additions & 10 deletions R/tm_t_shift_by_arm_by_worst.R
Original file line number Diff line number Diff line change
Expand Up @@ -179,8 +179,7 @@ template_shift_by_arm_by_worst <- function(dataname,
# Full table.
y$table <- substitute(
expr = {
result <- rtables::build_table(lyt = lyt, df = dataname)
result
table <- rtables::build_table(lyt = lyt, df = dataname)
},
env = list(dataname = as.name(dataname))
)
Expand All @@ -197,6 +196,14 @@ template_shift_by_arm_by_worst <- function(dataname,
#'
#' @inherit module_arguments return
#'
#' @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
Expand Down Expand Up @@ -278,7 +285,8 @@ tm_t_shift_by_arm_by_worst <- function(label,
total_label = default_total_label(),
pre_output = NULL,
post_output = NULL,
basic_table_args = teal.widgets::basic_table_args()) {
basic_table_args = teal.widgets::basic_table_args(),
decorators = NULL) {
if (lifecycle::is_present(base_var)) {
baseline_var <- base_var
warning(
Expand Down Expand Up @@ -307,8 +315,10 @@ tm_t_shift_by_arm_by_worst <- 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")
args <- as.list(environment())
decorators <- normalize_decorators(decorators)
assert_decorators(decorators, null.ok = TRUE, "table")

args <- as.list(environment())

data_extract_list <- list(
arm_var = cs_to_des_select(arm_var, dataname = parentname),
Expand All @@ -334,7 +344,8 @@ tm_t_shift_by_arm_by_worst <- function(label,
treatment_flag = treatment_flag,
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)
Expand Down Expand Up @@ -412,6 +423,7 @@ ui_shift_by_arm_by_worst <- function(id, ...) {
choices = c("ifany", "no"),
selected = a$useNA
),
ui_decorate_teal_data(ns("decorator"), decorators = select_decorators(a$decorators, "table")),
teal.widgets::panel_group(
teal.widgets::panel_item(
"Additional Variables Info",
Expand Down Expand Up @@ -456,7 +468,8 @@ srv_shift_by_arm_by_worst <- function(id,
na_level,
add_total,
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")
Expand Down Expand Up @@ -572,7 +585,7 @@ srv_shift_by_arm_by_worst <- function(id,
)
})

# generate r code for the analysis
# Generate r code for the analysis.
all_q <- reactive({
validate_checks()

Expand All @@ -597,18 +610,27 @@ srv_shift_by_arm_by_worst <- 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",
table_r = table_r
)

# 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
)

Expand All @@ -627,7 +649,7 @@ srv_shift_by_arm_by_worst <- 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)
Expand Down
24 changes: 23 additions & 1 deletion man/tm_t_shift_by_arm_by_worst.Rd

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