Spider plot Teal Module — tm_g_spiderplot • teal.osprey

Display spider plot as a shiny module

Usage

tm_g_spiderplot(
  label,
  dataname,
  paramcd = teal.picks::variables(choices = dplyr::starts_with("PARAMCD"), selected = 1L),
  x_var = teal.picks::variables(choices = dplyr::where(is.numeric), selected = 1L),
  y_var = teal.picks::variables(choices = teal.picks::is_categorical(), selected = 1L),
  marker_var = teal.picks::variables(choices = teal.picks::is_categorical(), selected =
    1L),
  line_colorby_var = teal.picks::variables(choices = teal.picks::is_categorical(),
    selected = 1L),
  xfacet_var = NULL,
  yfacet_var = NULL,
  vref_line = NULL,
  href_line = NULL,
  anno_txt_var = TRUE,
  legend_on = FALSE,
  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().
paramcd: 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. Variable value designating the studied parameter.
x_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. For x-axis variables.
y_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. For y-axis variables.
marker_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. For marker symbol.
line_colorby_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. For line color.
xfacet_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. For x facets.
yfacet_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. For y facets.
vref_line: vertical reference lines
href_line: horizontal reference lines
anno_txt_var: annotation text
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.

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_spiderplot(
   ..., # 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 <- within(teal_data(), {
  library(nestcolor)
  ADSL <- teal.data::rADSL
  ADTR <- teal.data::rADTR
})

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

app <- init(
  data = data,
  modules = modules(
    tm_g_spiderplot(
      label = "Spider plot (picks)",
      dataname = "ADTR",
      paramcd = variables(
        choices = "PARAMCD",
        selected = "PARAMCD"
      ),
      x_var = variables(
        choices = dplyr::where(is.numeric),
        selected = 1L
      ),
      y_var = variables(
        choices = c("PCHG", "CHG", "AVAL"),
        selected = "PCHG"
      ),
      marker_var = variables(
        choices = c("SEX", "RACE", "USUBJID"),
        selected = "SEX"
      ),
      line_colorby_var = variables(
        choices = c("SEX", "USUBJID", "RACE"),
        selected = "SEX"
      ),
      xfacet_var = variables(
        choices = c("SEX", "ARM"),
        selected = "SEX"
      ),
      yfacet_var = variables(
        choices = c("SEX", "ARM"),
        selected = "ARM"
      ),
      vref_line = "10, 37",
      href_line = "-20, 0"
    )
  )
)
#> Initializing tm_g_spiderplot
if (interactive()) {
  shinyApp(app$ui, app$server)
}