teal Module: Simple Bar Chart and Table of Counts per Category

This module produces a ggplot2::ggplot() type bar chart and summary table of counts per category.

Usage

tm_g_barchart_simple(
  x = NULL,
  fill = NULL,
  x_facet = NULL,
  y_facet = NULL,
  label = "Count Barchart",
  plot_options = NULL,
  plot_height = c(600L, 200L, 2000L),
  plot_width = NULL,
  pre_output = NULL,
  post_output = NULL,
  ggplot2_args = teal.widgets::ggplot2_args(),
  transformators = list(),
  decorators = list()
)

Arguments

x

(data_extract_spec)
variable on the x-axis.

fill

(data_extract_spec)
grouping variable to determine bar colors.

x_facet

(data_extract_spec)
row-wise faceting groups.

y_facet

(data_extract_spec)
column-wise faceting groups.

label

(character)
menu item label of the module in the teal app.

plot_options

(list)
list of plot options.

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.

Details

Categories can be defined up to four levels deep and are defined through the x, fill, x_facet, and y_facet parameters. Any parameters set to NULL (default) are ignored.

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_barchart_simple(
   ..., # 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

Examples

library(nestcolor)
library(dplyr)

data <- teal_data()
data <- within(data, {
  ADSL <- tmc_ex_adsl %>%
    mutate(ITTFL = factor("Y") %>%
      with_label("Intent-To-Treat Population Flag"))
  ADAE <- tmc_ex_adae %>%
    filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

ADSL <- data[["ADSL"]]
ADAE <- data[["ADAE"]]

app <- init(
  data = data,
  modules = modules(
    tm_g_barchart_simple(
      label = "ADAE Analysis",
      x = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          choices = variable_choices(
            ADSL,
            c(
              "ARM", "ACTARM", "SEX",
              "RACE", "ITTFL", "SAFFL", "STRATA2"
            )
          ),
          selected = "ACTARM",
          multiple = FALSE
        )
      ),
      fill = list(
        data_extract_spec(
          dataname = "ADSL",
          select = select_spec(
            choices = variable_choices(
              ADSL,
              c(
                "ARM", "ACTARM", "SEX",
                "RACE", "ITTFL", "SAFFL", "STRATA2"
              )
            ),
            selected = "SEX",
            multiple = FALSE
          )
        ),
        data_extract_spec(
          dataname = "ADAE",
          select = select_spec(
            choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
            selected = NULL,
            multiple = FALSE
          )
        )
      ),
      x_facet = list(
        data_extract_spec(
          dataname = "ADAE",
          select = select_spec(
            choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
            selected = "AETOXGR",
            multiple = FALSE
          )
        ),
        data_extract_spec(
          dataname = "ADSL",
          select = select_spec(
            choices = variable_choices(
              ADSL,
              c(
                "ARM", "ACTARM", "SEX",
                "RACE", "ITTFL", "SAFFL", "STRATA2"
              )
            ),
            selected = NULL,
            multiple = FALSE
          )
        )
      ),
      y_facet = list(
        data_extract_spec(
          dataname = "ADAE",
          select = select_spec(
            choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
            selected = "AESEV",
            multiple = FALSE
          )
        ),
        data_extract_spec(
          dataname = "ADSL",
          select = select_spec(
            choices = variable_choices(
              ADSL,
              c(
                "ARM", "ACTARM", "SEX",
                "RACE", "ITTFL", "SAFFL", "STRATA2"
              )
            ),
            selected = NULL,
            multiple = FALSE
          )
        )
      )
    )
  )
)
#> Initializing tm_g_barchart_simple
if (interactive()) {
  shinyApp(app$ui, app$server)
}