teal.modules.clinical (version 0.10.0)

tm_g_pp_therapy: teal Module: Patient Profile Therapy Table and Plot

Description

This module produces a patient profile therapy table and ggplot2::ggplot() type plot using ADaM datasets.

Usage

tm_g_pp_therapy(
  label,
  dataname = "ADCM",
  parentname = "ADSL",
  patient_col = "USUBJID",
  atirel = NULL,
  cmdecod = NULL,
  cmindc = NULL,
  cmdose = NULL,
  cmtrt = NULL,
  cmdosu = NULL,
  cmroute = NULL,
  cmdosfrq = NULL,
  cmstdy = NULL,
  cmendy = 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(),
  transformators = list(),
  decorators = list()
)

Value

a teal_module object.

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.

atirel

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

cmdecod

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

cmindc

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

cmdose

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

cmtrt

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

cmdosu

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

cmroute

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

cmdosfrq

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

cmstdy

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

cmendy

(teal.transform::choices_selected())
object with all available choices and preselected option for the CMENDY 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").

transformators

(list of teal_transform_module) that will be applied to transform module's data input. To learn more check vignette("transform-input-data", package = "teal").

decorators

(named list of lists of teal_transform_module) optional, decorator for tables or plots included in the module output reported. The decorators are applied to the respective output objects.

See section "Decorating Module" below for more details.

Decorating Module

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

• plot (ggplot)

• table (datatables - output of DT::datatable())

A Decorator is applied to the specific output using a named list of teal_transform_module objects. The name of this list corresponds to the name of the output to which the decorator is applied. See code snippet below:

tm_g_pp_therapy(
   ..., # arguments for module
   decorators = list(
     plot = teal_transform_module(...), # applied only to `plot` output
     table = teal_transform_module(...) # applied only to `table` output
   )
)

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

To learn more please refer to the vignette vignette("transform-module-output", package = "teal") or the teal::teal_transform_module() documentation.

Examples in Shinylive

example-1

Open in Shinylive

Examples

library(nestcolor)
library(dplyr)

data <- teal_data()
data <- within(data, {
  ADCM <- tmc_ex_adcm
  ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADCM$USUBJID)
  ADCM$CMASTDTM <- ADCM$ASTDTM
  ADCM$CMAENDTM <- ADCM$AENDTM
})

join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADCM")]
adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
join_keys(data)["ADCM", "ADCM"] <- adcm_keys

ADSL <- data[["ADSL"]]
ADCM <- data[["ADCM"]]

app <- init(
  data = data,
  modules = modules(
    tm_g_pp_therapy(
      label = "Therapy",
      dataname = "ADCM",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      atirel = choices_selected(
        choices = variable_choices(ADCM, "ATIREL"),
        selected = c("ATIREL")
      ),
      cmdecod = choices_selected(
        choices = variable_choices(ADCM, "CMDECOD"),
        selected = "CMDECOD"
      ),
      cmindc = choices_selected(
        choices = variable_choices(ADCM, "CMINDC"),
        selected = "CMINDC"
      ),
      cmdose = choices_selected(
        choices = variable_choices(ADCM, "CMDOSE"),
        selected = "CMDOSE"
      ),
      cmtrt = choices_selected(
        choices = variable_choices(ADCM, "CMTRT"),
        selected = "CMTRT"
      ),
      cmdosu = choices_selected(
        choices = variable_choices(ADCM, "CMDOSU"),
        selected = c("CMDOSU")
      ),
      cmroute = choices_selected(
        choices = variable_choices(ADCM, "CMROUTE"),
        selected = "CMROUTE"
      ),
      cmdosfrq = choices_selected(
        choices = variable_choices(ADCM, "CMDOSFRQ"),
        selected = "CMDOSFRQ"
      ),
      cmstdy = choices_selected(
        choices = variable_choices(ADCM, "ASTDY"),
        selected = "ASTDY"
      ),
      cmendy = choices_selected(
        choices = variable_choices(ADCM, "AENDY"),
        selected = "AENDY"
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}