teal.modules.general (version 0.8.0)

tm_outliers: teal module: Outliers analysis

Description

Module to analyze and identify outliers using different methods such as IQR, Z-score, and Percentiles, and offers visualizations including box plots, density plots, and cumulative distribution plots to help interpret the outliers.

Usage

tm_outliers(
  label = "Outliers Module",
  outlier_var = teal.picks::picks(teal.picks::datasets(),
    teal.picks::variables(is.numeric, 1L, multiple = FALSE)),
  categorical_var = teal.picks::picks(teal.picks::datasets(),
    teal.picks::variables(choices = teal.picks::is_categorical(min.len = 1, max.len =
    10), selected = 1L, multiple = TRUE)),
  ggtheme = c("gray", "bw", "linedraw", "light", "dark", "minimal", "classic", "void"),
  ggplot2_args = teal.widgets::ggplot2_args(),
  plot_height = c(600, 200, 2000),
  plot_width = NULL,
  pre_output = NULL,
  post_output = NULL,
  transformators = list(),
  decorators = list()
)

Value

Object of class teal_module to be used in teal applications.

Arguments

label

(character(1)) Label shown in the navigation item for the module or module group. For modules() defaults to "root". See Details.

outlier_var

(picks or list of multiple picks) Specifies variable(s) to be analyzed for outliers.

categorical_var

(picks or list of multiple picks) optional, specifies the categorical variable(s) to split the selected outlier variables on.

ggtheme

(character) optional, ggplot2 theme to be used by default. Defaults to "gray".

ggplot2_args

(ggplot2_args) optional, object created by teal.widgets::ggplot2_args() with settings for all the plots or named list of ggplot2_args objects for plot-specific settings. The argument is merged with options variable teal.ggplot2_args and default module setup.

List names should match the following: c("default", "Boxplot", "Density Plot", "Cumulative Distribution Plot").

For more details see the vignette: vignette("custom-ggplot2-arguments", package = "teal.widgets").

plot_height

(numeric) optional, specifies the plot height as a three-element vector of value, min, and max intended for use with a slider UI element.

plot_width

(numeric) optional, specifies the plot width as a three-element vector of value, min, and max for a slider encoding the plot width.

pre_output

(shiny.tag) optional, text or UI element to be displayed before the module's output, providing context or a title. with text placed before the output to put the output into context. For example a title.

post_output

(shiny.tag) optional, text or UI element to be displayed after the module's output, adding context or further instructions. Elements like shiny::helpText() are useful.

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.

Decorating Module

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

• box_plot (ggplot)

• density_plot (ggplot)

• cumulative_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_outliers(
   ..., # arguments for module
   decorators = list(
     box_plot = teal_transform_module(...), # applied only to `box_plot` output
     density_plot = teal_transform_module(...), # applied only to `density_plot` output
     cumulative_plot = teal_transform_module(...) # applied only to `cumulative_plot` output
   )
)

For additional details and examples of decorators, refer to the vignette vignette("decorate-module-output", package = "teal.modules.general").

To learn more please refer to the vignette vignette("transform-module-output", package = "teal") or the teal::teal_transform_module() documentation.

Reporting

This module returns an object of class teal_module, that contains a server function. Since the server function returns a teal_report object, this makes this module reportable, which means that the reporting functionality will be turned on automatically by the teal framework.

For more information on reporting in teal, see the vignettes:

• vignette("reportable-shiny-application", package = "teal.reporter")

• vignette("adding-support-for-reporting-to-custom-modules", package = "teal")

Examples in Shinylive

example-1

Open in Shinylive

example-2

Open in Shinylive

Examples

# general data example
data <- teal_data()
data <- within(data, CO2 <- CO2)

app <- init(
  data = data,
  modules = modules(
    tm_outliers(
      outlier_var = teal.picks::picks(
        datasets("CO2", "CO2"),
        teal.picks::variables(c("conc", "uptake"), "uptake"),
        teal.picks::values()
      ),
      categorical_var = teal.picks::picks(
        datasets("CO2", "CO2"),
        teal.picks::variables(c("Plant", "Type", "Treatment"), "Plant"),
        teal.picks::values()
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}


# CDISC data example
data <- teal_data()
data <- within(data, {
  ADSL <- teal.data::rADSL
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_outliers(
      outlier_var = teal.picks::picks(
        datasets("ADSL", "ADSL"),
        teal.picks::variables(c("AGE", "BMRKR1"), "AGE")
      ),
      categorical_var = teal.picks::picks(
        datasets("ADSL", "ADSL"),
        teal.picks::variables(teal.picks::is_categorical(min.len = 1, max.len = 10))
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}