teal Module: Patient Profile Adverse Events Table and Plot — tm_g_pp_adverse

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()
)

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: optional, (numeric)
a 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: optional, (numeric)
a 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: optional, (shiny.tag)
with text placed before the output to put the output into context. For example a title.
post_output: optional, (shiny.tag)
with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.
ggplot2_args: optional, (ggplot2_args)
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").

Value

a teal_module object.

Examples

library(nestcolor)
library(dplyr)

ADAE <- tmc_ex_adae
ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADAE$USUBJID)

app <- init(
  data = cdisc_data(
    ADSL = ADSL,
    ADAE = ADAE,
    code = "
      ADAE <- tmc_ex_adae
      ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADAE$USUBJID)
    "
  ),
  modules = modules(
    tm_g_pp_adverse_events(
      label = "Adverse Events",
      dataname = "ADAE",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      aeterm = choices_selected(
        choices = variable_choices(ADAE, "AETERM"),
        selected = "AETERM"
      ),
      tox_grade = choices_selected(
        choices = variable_choices(ADAE, "AETOXGR"),
        selected = "AETOXGR"
      ),
      causality = choices_selected(
        choices = variable_choices(ADAE, "AEREL"),
        selected = "AEREL"
      ),
      outcome = choices_selected(
        choices = variable_choices(ADAE, "AEOUT"),
        selected = "AEOUT"
      ),
      action = choices_selected(
        choices = variable_choices(ADAE, "AEACN"),
        selected = "AEACN"
      ),
      time = choices_selected(
        choices = variable_choices(ADAE, "ASTDY"),
        selected = "ASTDY"
      ),
      decod = NULL
    )
  )
)
#> [INFO] 2024-02-26 01:42:35.5390 pid:1518 token:[] teal.modules.clinical Initializing tm_g_pp_adverse_events
if (interactive()) {
  shinyApp(app$ui, app$server)
}