teal.modules.clinical (version 0.9.0)

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()
)

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

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").

Examples

library(nestcolor)
library(dplyr)

ADCM <- tmc_ex_adcm
ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADCM$USUBJID)
ADCM$CMASTDTM <- ADCM$ASTDTM
ADCM$CMAENDTM <- ADCM$AENDTM
adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")

join_keys <- default_cdisc_join_keys[c("ADSL", "ADCM")]
join_keys["ADCM", "ADCM"] <- adcm_keys

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