teal.modules.clinical (version 0.9.0)

tm_g_ipp: teal Module: Individual Patient Plots

Description

This module produces ggplot2::ggplot() type individual patient plots that display trends in parameter values over time for each patient, using data with ADaM structure.

Usage

tm_g_ipp(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var,
  paramcd,
  id_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    "USUBJID"), "USUBJID", fixed = TRUE),
  visit_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    "AVISIT"), "AVISIT", fixed = TRUE),
  aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    "AVAL"), "AVAL", fixed = TRUE),
  avalu_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    "AVALU"), "AVALU", fixed = TRUE),
  base_var = lifecycle::deprecated(),
  baseline_var =
    teal.transform::choices_selected(teal.transform::variable_choices(dataname, "BASE"),
    "BASE", fixed = TRUE),
  add_baseline_hline = FALSE,
  separate_by_obs = FALSE,
  suppress_legend = FALSE,
  add_avalu = TRUE,
  plot_height = c(1200L, 400L, 5000L),
  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.

arm_var

(teal.transform::choices_selected())
object with all available choices and preselected option for variable values that can be used as arm variable.

paramcd

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

id_var

(teal.transform::choices_selected())
object specifying the variable name for subject id.

visit_var

(teal.transform::choices_selected())
object with all available choices and preselected option for variable names that can be used as visit variable. Must be a factor in dataname.

aval_var

(teal.transform::choices_selected())
object with all available choices and pre-selected option for the analysis variable.

avalu_var

(teal.transform::choices_selected())
object with all available choices and preselected option for the analysis unit variable.

base_var

Please use the baseline_var argument instead.

baseline_var

(teal.transform::choices_selected())
object with all available choices and preselected option for variable values that can be used as baseline_var.

add_baseline_hline

(logical)
whether a horizontal line should be added to the plot at baseline y-value.

separate_by_obs

(logical)
whether to create multi-panel plots.

suppress_legend

(logical)
whether to suppress the plot legend.

add_avalu

(logical)
whether avalu_first text should be appended to the plot title and y-axis label.

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. For this module, this argument will only accept ggplot2_args object with labs list of the following child elements: title, subtitle, x, y. No other elements are taken into account. 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").

See Also

The TLG Catalog where additional example apps implementing this module can be found.

Examples

library(nestcolor)
library(dplyr)

ADSL <- tmc_ex_adsl %>%
  slice(1:20) %>%
  df_explicit_na()
ADLB <- tmc_ex_adlb %>%
  filter(USUBJID %in% ADSL$USUBJID) %>%
  df_explicit_na() %>%
  filter(AVISIT != "SCREENING")

app <- init(
  data = cdisc_data(
    ADSL = ADSL,
    ADLB = ADLB,
    code = "
      ADSL <- tmc_ex_adsl %>% slice(1:20) %>% df_explicit_na()
      ADLB <- tmc_ex_adlb %>% filter(USUBJID %in% ADSL$USUBJID) %>%
        df_explicit_na() %>% filter(AVISIT != \"SCREENING\")
    "
  ),
  modules = modules(
    tm_g_ipp(
      label = "Individual Patient Plot",
      dataname = "ADLB",
      arm_var = choices_selected(
        value_choices(ADLB, "ARMCD"),
        "ARM A"
      ),
      paramcd = choices_selected(
        value_choices(ADLB, "PARAMCD"),
        "ALT"
      ),
      aval_var = choices_selected(
        variable_choices(ADLB, c("AVAL", "CHG")),
        "AVAL"
      ),
      avalu_var = choices_selected(
        variable_choices(ADLB, c("AVALU")),
        "AVALU",
        fixed = TRUE
      ),
      id_var = choices_selected(
        variable_choices(ADLB, c("USUBJID")),
        "USUBJID",
        fixed = TRUE
      ),
      visit_var = choices_selected(
        variable_choices(ADLB, c("AVISIT")),
        "AVISIT"
      ),
      baseline_var = choices_selected(
        variable_choices(ADLB, c("BASE")),
        "BASE",
        fixed = TRUE
      ),
      add_baseline_hline = FALSE,
      separate_by_obs = FALSE
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}