teal Module: Patient Profile Therapy Table and Plot — tm_g_pp

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()
)

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").

Value

a teal_module object.

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$AENDTM
    ",
    join_keys = join_keys
  ),
  modules = modules(
    tm_g_pp_therapy(
      label = "Therapy",
      dataname = "ADCM",
      parentname = "ADSL",
      patient_col = "USUBJID",
      plot_height = c(600L, 200L, 2000L),
      atirel = choices_selected(
        choices = variable_choices(ADCM, "ATIREL"),
        selected = c("ATIREL")
      ),
      cmdecod = choices_selected(
        choices = variable_choices(ADCM, "CMDECOD"),
        selected = "CMDECOD"
      ),
      cmindc = choices_selected(
        choices = variable_choices(ADCM, "CMINDC"),
        selected = "CMINDC"
      ),
      cmdose = choices_selected(
        choices = variable_choices(ADCM, "CMDOSE"),
        selected = "CMDOSE"
      ),
      cmtrt = choices_selected(
        choices = variable_choices(ADCM, "CMTRT"),
        selected = "CMTRT"
      ),
      cmdosu = choices_selected(
        choices = variable_choices(ADCM, "CMDOSU"),
        selected = c("CMDOSU")
      ),
      cmroute = choices_selected(
        choices = variable_choices(ADCM, "CMROUTE"),
        selected = "CMROUTE"
      ),
      cmdosfrq = choices_selected(
        choices = variable_choices(ADCM, "CMDOSFRQ"),
        selected = "CMDOSFRQ"
      ),
      cmstdy = choices_selected(
        choices = variable_choices(ADCM, "ASTDY"),
        selected = "ASTDY"
      ),
      cmendy = choices_selected(
        choices = variable_choices(ADCM, "AENDY"),
        selected = "AENDY"
      )
    )
  )
)
#> [INFO] 2024-02-26 01:42:36.6546 pid:1518 token:[] teal.modules.clinical Initializing tm_g_pp_therapy
if (interactive()) {
  shinyApp(app$ui, app$server)
}