teal.modules.general (version 0.8.0)

tm_a_regression: teal module: Scatterplot and regression analysis

Description

Module for visualizing regression analysis, including scatterplots and various regression diagnostics plots. It allows users to explore the relationship between a set of regressors and a response variable, visualize residuals, and identify outliers.

Usage

tm_a_regression(
  label = "Regression Analysis",
  regressor = teal.picks::picks(teal.picks::datasets(), teal.picks::variables(choices =
    is.numeric, selected = tidyselect::last_col(), multiple = TRUE)),
  response,
  outlier,
  plot_height = c(600, 200, 2000),
  plot_width = NULL,
  alpha = c(1, 0, 1),
  size = c(2, 1, 8),
  ggtheme = c("gray", "bw", "linedraw", "light", "dark", "minimal", "classic", "void"),
  ggplot2_args = teal.widgets::ggplot2_args(),
  pre_output = NULL,
  post_output = NULL,
  default_plot_type = 1,
  default_outlier_label = "USUBJID",
  label_segment_threshold = c(0.5, 0, 10),
  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.

regressor

(picks) Specification for regressor variables selection. Created using teal.picks::picks(), which allows selecting variables to use as regressors in the regression model. teal.picks::variables(multiple = TRUE) allowed.

response

(picks) Specification for response variable selection. Created using teal.picks::picks(), which allows selecting a single numeric variable to use as the response in the regression model. teal.picks::variables(multiple = TRUE) not allowed.

outlier

(picks) Optional specification for outlier label variable selection. Created using teal.picks::picks(), which allows selecting a factor or character variable to label outlier points on the plots.

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.

alpha

(integer(1) or integer(3)) optional, specifies point opacity.

• When the length of alpha is one: the plot points will have a fixed opacity.

• When the length of alpha is three: the plot points opacity are dynamically adjusted based on vector of value, min, and max.

size

(integer(1) or integer(3)) optional, specifies point size.

• When the length of size is one: the plot point sizes will have a fixed size.

• When the length of size is three: the plot points size are dynamically adjusted based on vector of value, min, and max.

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", "Response vs Regressor", "Residuals vs Fitted", "Scale-Location", "Cook's distance", "Residuals vs Leverage", "Cook's dist vs Leverage").

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

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.

default_plot_type

(numeric) optional, defaults to "Response vs Regressor".

1. Response vs Regressor

2. Residuals vs Fitted

3. Normal Q-Q

4. Scale-Location

5. Cook's distance

6. Residuals vs Leverage

7. Cook's dist vs Leverage

default_outlier_label

(character) optional, default column selected to label outliers.

label_segment_threshold

(numeric(1) or numeric(3)) Minimum distance between label and point on the plot that triggers the creation of a line segment between the two. This may happen when the label cannot be placed next to the point as it overlaps another label or point. The value is used as the min.segment.length parameter to the ggrepel::geom_text_repel() function.

It can take the following forms:

• numeric(1): Fixed value used for the minimum distance and the slider is not presented in the UI.

• numeric(3): A slider is presented in the UI (under "Plot settings") to adjust the minimum distance dynamically.

  It takes the form of c(value, min, max) and it is passed to the value_min_max argument in teal.widgets::optionalSliderInputValMinMax.

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:

• 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_a_regression(
   ..., # arguments for module
   decorators = list(
     plot = teal_transform_module(...) # applied to the `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, {
  require(nestcolor)
  CO2 <- CO2
})

app <- init(
  data = data,
  modules = modules(
    tm_a_regression(
      label = "Regression",
      response = teal.picks::picks(
        datasets("CO2"),
        teal.picks::variables(choices = "uptake", selected = "uptake")
      ),
      regressor = teal.picks::picks(
        datasets("CO2"),
        teal.picks::variables(choices = c("conc", "Treatment"), selected = "conc", multiple = TRUE)
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}

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

app <- init(
  data = data,
  modules = modules(
    tm_a_regression(
      label = "Regression",
      response = teal.picks::picks(
        datasets("ADSL"),
        teal.picks::variables(choices = "BMRKR1", selected = "BMRKR1")
      ),
      regressor = teal.picks::picks(
        datasets("ADSL"),
        teal.picks::variables(choices = c("AGE", "SEX", "RACE"), selected = "AGE", multiple = TRUE)
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}