tm_g_ci: teal Module: Confidence Interval Plot

In teal.modules.clinical: 'teal' Modules for Standard Clinical Outputs

teal Module: Confidence Interval Plot

Description

This module produces a ggplot2::ggplot() type confidence interval plot consistent with the TLG Catalog template CIG01 available here.

Usage

tm_g_ci(
  label,
  x_var,
  y_var,
  color,
  stat = c("mean", "median"),
  conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =
    TRUE),
  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()
)

Arguments

label	(character) menu item label of the module in the teal app.
x_var	(character) name of the treatment variable to put on the x-axis.
y_var	(character) name of the response variable to put on the y-axis.
color	(data_extract_spec) the group variable used to determine the plot colors, shapes, and line types.
stat	(character) statistic to plot. Options are "mean" and "median".
conf_level	(teal.transform::choices_selected()) object with all available choices and pre-selected option for the confidence level, each within range of (0, 1).
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.

Value

a teal_module object.

Decorating Module

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

• plot (ggplot)

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

See Also

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

Examples

library(nestcolor)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl
  ADLB <- tmc_ex_adlb
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

app <- init(
  data = data,
  modules = modules(
    tm_g_ci(
      label = "Confidence Interval Plot",
      x_var = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          choices = c("ARMCD", "BMRKR2"),
          selected = c("ARMCD"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      y_var = data_extract_spec(
        dataname = "ADLB",
        filter = list(
          filter_spec(
            vars = "PARAMCD",
            choices = levels(ADLB$PARAMCD),
            selected = levels(ADLB$PARAMCD)[1],
            multiple = FALSE,
            label = "Select lab:"
          ),
          filter_spec(
            vars = "AVISIT",
            choices = levels(ADLB$AVISIT),
            selected = levels(ADLB$AVISIT)[1],
            multiple = FALSE,
            label = "Select visit:"
          )
        ),
        select = select_spec(
          label = "Analyzed Value",
          choices = c("AVAL", "CHG"),
          selected = "AVAL",
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      color = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Color by variable",
          choices = c("SEX", "STRATA1", "STRATA2"),
          selected = c("STRATA1"),
          multiple = FALSE,
          fixed = FALSE
        )
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

teal.modules.clinical documentation built on April 4, 2025, 12:35 a.m.