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Teal Module for Waterfall Plot

Source: R/tm_g_waterfall.R
tm_g_waterfall.Rd

This is teal module that generates a waterfall plot for ADaM data

Usage 

tm_g_waterfall(
  label,
  parentname = "ADSL",
  dataname_tr = "ADTR",
  dataname_rs = "ADRS",
  bar_paramcd = teal.picks::values(choices = teal.picks::is_categorical(), multiple =
    FALSE),
  bar_var = teal.picks::variables(choices = is.numeric, multiple = FALSE),
  bar_color_var = teal.picks::variables(choices = teal.picks::is_categorical(max.len =
    20), selected = NULL),
  bar_color_opt = NULL,
  sort_var = teal.picks::variables(selected = NULL),
  add_label_var_sl = teal.picks::variables(selected = NULL),
  add_label_paramcd_rs = teal.picks::values(selected = NULL, multiple = FALSE),
  anno_txt_var_sl = teal.picks::variables(selected = NULL, multiple = TRUE),
  anno_txt_paramcd_rs = teal.picks::values(selected = NULL),
  facet_var = teal.picks::variables(selected = NULL),
  ytick_at = 20,
  href_line = NULL,
  gap_point_val = NULL,
  show_value = TRUE,
  plot_height = c(1200L, 400L, 5000L),
  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.

parentname

(character(1))
analysis data used for several variables in the teal module, needs to be available in the list passed to the data argument of teal::init(). The default is "ADSL"

dataname_tr

(character(1)) tumor burden analysis data used in teal module to plot as bar height, needs to be available in the list passed to the data argument of teal::init()

dataname_rs

(character(1)) response analysis data used in teal module to label response parameters, needs to be available in the list passed to the data argument of teal::init()

bar_paramcd

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. Parameter in tumor burden data that will be plotted as bar height.

bar_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. Numeric variable from dataset to plot the bar height, e.g., PCHG.

bar_color_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. Color by variable (subject level). Defaults to no selection.

bar_color_opt

aesthetic values to map color values (named vector to map color values to each name). If not NULL, please make sure this contains all possible values for bar_color_var values, otherwise color will be assigned by ggplot default, please note that NULL needs to be specified in this case

sort_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. Sort by variable (subject level). Defaults to no selection.

add_label_var_sl

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. Add label to bars (subject level).

add_label_paramcd_rs

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. Add label to bars (response dataset). At least one of add_label_var_sl and add_label_paramcd_rs needs to not be selected.

anno_txt_var_sl

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. Subject level variables to be displayed in the annotation table, default is no selection.

anno_txt_paramcd_rs

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. Analysis dataset variables to be displayed in the annotation table, default is no selection.

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. Facet by variable (subject level). Defaults to no selection.

ytick_at

(numeric(1)) bar height axis interval, default is 20

href_line

(numeric) numeric vector to plot horizontal reference lines, default is NULL

gap_point_val

(numeric(1)) singular numeric value for adding bar break when some bars are significantly higher than others, default is NULL

show_value

(logical(1)) boolean of whether value of bar height is shown, default is TRUE

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

[Experimental] (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 (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:

Author

Ting Qi (qit3) qit3@gene.com

houx14 houx14@gene.com

Examples 

data <- within(teal_data(), {
  library(nestcolor)
  ADSL <- teal.data::rADSL
  ADRS <- teal.data::rADRS
  ADTR <- teal.data::rADTR
  ADSL$SEX <- factor(ADSL$SEX, levels = unique(ADSL$SEX))
})

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

app <- init(
  data = data,
  modules = modules(
    tm_g_waterfall(
      label = "Waterfall",
      dataname_tr = "ADTR",
      dataname_rs = "ADRS",
      bar_paramcd = values(c("SLDINV"), "SLDINV", multiple = FALSE),
      bar_var = variables(c("PCHG", "AVAL"), "PCHG"),
      bar_color_var = variables(c("ARMCD", "SEX"), "ARMCD"),
      bar_color_opt = NULL,
      sort_var = variables(c("ARMCD", "SEX"), NULL),
      add_label_var_sl = variables(c("SEX", "EOSDY"), NULL),
      add_label_paramcd_rs = values(c("BESRSPI", "OBJRSPI"), NULL, multiple = FALSE),
      anno_txt_var_sl = variables(c("SEX", "ARMCD", "BMK1", "BMK2"), NULL, multiple = TRUE),
      anno_txt_paramcd_rs = values(c("BESRSPI", "OBJRSPI"), NULL),
      facet_var = variables(c("SEX", "ARMCD", "STRATA1", "STRATA2"), NULL),
      href_line = "-30, 20"
    )
  )
)
#> Initializing tm_g_waterfall
if (interactive()) {
  shinyApp(app$ui, app$server)
}