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teal Module: Patient Profile Adverse Events Table and Plot

Source: R/tm_g_pp_adverse_events.R
tm_g_pp_adverse_events.Rd

This module produces an adverse events table and ggplot2::ggplot() type plot using ADaM datasets.

Usage 

tm_g_pp_adverse_events(
  label,
  dataname = "ADAE",
  parentname = "ADSL",
  patient_col = "USUBJID",
  aeterm = NULL,
  tox_grade = NULL,
  causality = NULL,
  outcome = NULL,
  action = NULL,
  time = NULL,
  decod = NULL,
  font_size = c(12L, 12L, 25L),
  plot_height = c(700L, 200L, 2000L),
  plot_width = NULL,
  pre_output = NULL,
  post_output = NULL,
  ggplot2_args = teal.widgets::ggplot2_args(),
  decorators = NULL
)

Arguments

label

(character)
menu item label of the module in the teal app.

dataname

(character)
analysis data used in teal module.

parentname

(character)
parent analysis data used in teal module, usually this refers to ADSL.

patient_col

(character)
name of patient ID variable.

aeterm

(teal.transform::choices_selected())
object with all available choices and preselected option for the AETERM variable from dataname.

tox_grade

(teal.transform::choices_selected())
object with all available choices and preselected option for the AETOXGR variable from dataname.

causality

(teal.transform::choices_selected())
object with all available choices and preselected option for the AEREL variable from dataname.

outcome

(teal.transform::choices_selected())
object with all available choices and preselected option for the AEOUT variable from dataname.

action

(teal.transform::choices_selected())
object with all available choices and preselected option for the AEACN variable from dataname.

time

(teal.transform::choices_selected())
object with all available choices and preselected option for the ASTDY variable from dataname.

decod

(teal.transform::choices_selected())
object with all available choices and preselected option for the AEDECOD variable from dataname.

font_size

(numeric)
numeric vector of length 3 of current, minimum and maximum font size values.

plot_height

(numeric) optional
vector of length three with c(value, min, max). Specifies the height of the main plot and renders a slider on the plot to interactively adjust the plot height.

plot_width

(numeric) optional
vector of length three with c(value, min, max). Specifies the width of the main plot and renders a slider on the plot to interactively adjust the plot width.

pre_output

(shiny.tag) optional,
with text placed before the output to put the output into context. For example a title.

post_output

(shiny.tag) optional,
with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.

ggplot2_args

(ggplot2_args) optional
object created by teal.widgets::ggplot2_args() with settings for the module plot. The argument is merged with option teal.ggplot2_args and with default module arguments (hard coded in the module body). For more details, see the vignette: vignette("custom-ggplot2-arguments", package = "teal.widgets").

decorators

[Experimental] " (list of teal_transform_module, named list of teal_transform_module or" NULL) optional, if not NULL, decorator for tables or plots included in the module. When a named list of 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 default.

See section "Decorating Module" below for more details.

Value

a teal_module object.

Decorating Modules

This module generates the following objects, which can be modified in place using decorators::

Decorators can be applied to all outputs or only to specific objects using a named list of teal_transform_module objects. The "default" name is reserved for decorators that are applied to all outputs. See code snippet below:

tm_g_pp_adverse_events(
   ..., # arguments for module
   decorators = list(
     default = list(teal_transform_module(...)), # applied to all outputs
     plot = list(teal_transform_module(...)), # applied only to `plot` output
     table = list(teal_transform_module(...)) # applied only to `table` output
   )
)

For additional details and examples of decorators, refer to the vignette vignette("decorate-modules-output", package = "teal") or the teal_transform_module() documentation.

Examples in Shinylive

example-1

Open in Shinylive

Examples 

library(nestcolor)
library(dplyr)

data <- teal_data()
data <- within(data, {
  ADAE <- tmc_ex_adae
  ADSL <- tmc_ex_adsl %>%
    filter(USUBJID %in% ADAE$USUBJID)
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

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

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
    )
  )
)
#> Initializing tm_g_pp_adverse_events
#> Initializing reporter_previewer_module
if (interactive()) {
  shinyApp(app$ui, app$server)
}