Teal Module: Patient Profile Therapy Teal Module — tm_g_pp

This teal module produces a patient profile therapy 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)
patient ID column to be used.

atirel

(teal.transform::choices_selected() or teal.transform::data_extract_spec())
ATIREL column of the ADCM dataset.

cmdecod

(teal.transform::choices_selected() or teal.transform::data_extract_spec())
CMDECOD column of the ADCM dataset.

cmindc

(teal.transform::choices_selected() or teal.transform::data_extract_spec())
CMINDC column of the ADCM dataset.

cmdose

(teal.transform::choices_selected() or teal.transform::data_extract_spec())
CMDOSE column of the ADCM dataset.

cmtrt

(teal.transform::choices_selected() or teal.transform::data_extract_spec())
CMTRT column of the ADCM dataset.

cmdosu

(teal.transform::choices_selected() or teal.transform::data_extract_spec())
CMDOSU column of the ADCM dataset.

cmroute

(teal.transform::choices_selected() or teal.transform::data_extract_spec())
CMROUTE column of the ADCM dataset.

cmdosfrq

(teal.transform::choices_selected() or teal.transform::data_extract_spec())
CMDOSFRQ column of the ADCM dataset.

cmstdy

(teal.transform::choices_selected() or teal.transform::data_extract_spec())
CMSTDY column of the ADCM dataset.

cmendy

(teal.transform::choices_selected() or teal.transform::data_extract_spec())
CMENDY column of the ADCM dataset.

font_size

(numeric)
numeric vector of length 3 for current, min and max 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 help vignette: vignette("custom-ggplot2-arguments", package = "teal.widgets").

Examples

library(scda)
library(nestcolor)

synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
ADSL <- synthetic_cdisc_data_latest$adsl
ADCM <- synthetic_cdisc_data_latest$adcm

#' Modify ADCM
ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD))
ADCM$CMDOSE <- 1
ADCM$CMTRT <- ADCM$CMCAT
ADCM$CMDOSU <- "U"
ADCM$CMROUTE <- "CMROUTE"
ADCM$CMDOSFRQ <- "CMDOSFRQ"
ADCM$CMASTDTM <- ADCM$ASTDTM
ADCM$CMAENDTM <- ADCM$AENDTM
formatters::var_labels(
  ADCM[c("CMINDC", "CMTRT", "ASTDY", "AENDY")]
) <- c(
  "Indication",
  "Reported Name of Drug, Med, or Therapy",
  "Study Day of Start of Medication",
  "Study Day of End of Medication"
)
adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")

app <- init(
  data = cdisc_data(
    cdisc_dataset("ADSL", ADSL,
      code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
        ADSL <- synthetic_cdisc_data_latest$adsl"
    ),
    cdisc_dataset("ADCM", ADCM,
      code = "ADCM <- synthetic_cdisc_data('latest')$adcm
        ADCM$CMINDC <- paste0('Indication_', as.numeric(ADCM$CMDECOD))
        ADCM$CMDOSE <- 1
        ADCM$CMTRT <- ADCM$CMCAT
        ADCM$CMDOSU <- 'U'
        ADCM$CMROUTE <- 'CMROUTE'
        ADCM$CMDOSFRQ <- 'CMDOSFRQ'
        ADCM$CMASTDTM <- ADCM$ASTDTM
        ADCM$CMAENDTM <- ADCM$AENDTM
        formatters::var_labels(
          ADCM[c('CMINDC', 'CMTRT', 'ASTDY', 'AENDY')]) <- c(
            'Indication',
            'Reported Name of Drug, Med, or Therapy',
            'Study Day of Start of Medication',
            'Study Day of End of Medication')
        ADCM",
      keys = adcm_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] 2022-10-14 09:10:11.5935 pid:3139 token:[] teal.modules.clinical Initializing tm_g_pp_therapy
if (FALSE) {
shinyApp(app$ui, app$server)
}