Butterfly plot Teal Module — tm_g_butterfly • teal.osprey

Display butterfly plot as a shiny module

Usage

tm_g_butterfly(
  label,
  dataname,
  filter_var = NULL,
  right_var = teal.picks::variables(is.factor),
  left_var = teal.picks::variables(is.factor),
  category_var = teal.picks::variables(teal.picks::is_categorical()),
  color_by_var = teal.picks::variables(dplyr::starts_with("AETO")),
  count_by_var = teal.picks::values(choices = c("# of patients", "# of AEs"), selected =
    "# of patients"),
  facet_var = NULL,
  sort_by_var = teal.picks::values(choices = c("count", "alphabetical"), selected =
    "count"),
  legend_on = TRUE,
  plot_height = c(600L, 200L, 2000L),
  plot_width = NULL,
  pre_output = NULL,
  post_output = NULL,
  transformators = list(),
  decorators = list()
)

Arguments

label: (character(1)) Label shown in the navigation item for the module or module group. For modules() defaults to "root". See Details.
dataname: (character(1))
analysis data used in the teal module, needs to be available in the list passed to the data argument of teal::init().
filter_var: Either a (teal.picks::variables()) object or a (teal.transform::choices_selected()) object. choices_selected() is being deprecated as an argument type and will be removed in the future. Object with variable name of data filter, please see details regarding expected values, default is NULL.
right_var: Either a (teal.picks::variables()) object or a (teal.transform::choices_selected()) object. choices_selected() is being deprecated as an argument type and will be removed in the future. Object with dichotomization variable for the right side.
left_var: Either a (teal.picks::variables()) object or a (teal.transform::choices_selected()) object. choices_selected() is being deprecated as an argument type and will be removed in the future. Object with dichotomization variable for the left side.
category_var: Either a (teal.picks::variables()) object or a (teal.transform::choices_selected()) object. choices_selected() is being deprecated as an argument type and will be removed in the future. Object with category (y-axis) variable.
color_by_var: Either a (teal.picks::variables()) object or a (teal.transform::choices_selected()) object. choices_selected() is being deprecated as an argument type and will be removed in the future. Object with variable that defines color blocks within each bar.
count_by_var: Either a (teal.picks::values()) object or a (teal.transform::choices_selected()) object. choices_selected() is being deprecated as an argument type and will be removed in the future. Object with variable that defines how the x axis is calculated.
facet_var: Either a (teal.picks::variables()) object or a (teal.transform::choices_selected()) object. choices_selected() is being deprecated as an argument type and will be removed in the future. Object with variable for row facets.
sort_by_var: Either a (teal.picks::values()) object or a (teal.transform::choices_selected()) object. choices_selected() is being deprecated as an argument type and will be removed in the future. Object with argument for order of class and term elements in table, default here is "count".
legend_on: (boolean) value for whether legend is displayed
plot_height: (numeric(3))
vector to indicate default value, minimum and maximum values.
plot_width: (numeric(3))
vector to indicate default value, minimum and maximum values.
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.
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 teal_transform_module) optional, decorators for the module plot output.

Value

the teal::module() object.

Details

filter_var option is designed to work in conjunction with filtering function provided by teal (encoding panel on the right hand side of the shiny app). It can be used as quick access to predefined subsets of the domain datasets (not subject-level dataset) to be used for analysis, denoted by an value of "Y". Each variable within the filter_var_choices is expected to contain values of either "Y" or "N". If multiple variables are selected as filter_var, only observations with "Y" value in each and every selected variables will be used for subsequent analysis. Flag variables (from ADaM datasets) can be used directly as filter.

Decorating Module

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

plot (grob, gtable)

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_butterfly(
   ..., # 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")

Author

Carolyn Zhang (zhanc107) carolyn.zhang@duke.edu

Chendi Liao (liaoc10) chendi.liao@roche.com

Examples

data <- teal_data() %>%
  eval_code("set.seed(23) # @linksto ADSL") %>%
  within({
    library(nestcolor)
    library(dplyr)
    ADSL <- teal.data::rADSL
    ADAE <- teal.data::rADAE
    ADSL <- mutate(ADSL, DOSE = paste(sample(1:3, n(), replace = TRUE), "UG"))
    ADAE <- mutate(
      ADAE,
      flag1 = ifelse(AETOXGR == 1, 1, 0),
      flag2 = ifelse(AETOXGR == 2, 1, 0),
      flag3 = ifelse(AETOXGR == 3, 1, 0),
      flag1_filt = rep("Y", n())
    )
  })

join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_g_butterfly(
      label = "Butterfly Plot",
      dataname = "ADAE",
      right_var = variables(
        choices = c("SEX", "ARM", "RACE"),
        selected = "SEX"
      ),
      left_var = variables(
        choices = c("SEX", "ARM", "RACE"),
        selected = "RACE"
      ),
      category_var = variables(
        choices = c("AEDECOD", "AEBODSYS"),
        selected = "AEBODSYS"
      ),
      color_by_var = variables(
        choices = c("AETOXGR"),
        selected = "AETOXGR",
        "allow-clear" = TRUE,
        fixed = FALSE
      ),
      count_by_var = values(
        choices = c("# of patients", "# of AEs"),
        selected = "# of patients"
      ),
      facet_var = variables(
        choices = c("RACE", "SEX", "ARM"),
        selected = NULL
      ),
      sort_by_var = values(
        choices = c("count", "alphabetical"),
        selected = "count"
      )
    )
  )
)
#> Initializing tm_g_butterfly
if (interactive()) {
  shinyApp(app$ui, app$server)
}