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Teal Module for Swimlane Plot

Source: R/tm_g_swimlane.R
tm_g_swimlane.Rd

This is a teal module that generates a swimlane plot (bar plot with markers) for ADaM data

Usage 

tm_g_swimlane(
  label,
  dataname,
  bar_var = teal.picks::variables(choices = is.numeric, selected = 1L),
  parentname = "ADSL",
  bar_color_var = NULL,
  sort_var = NULL,
  marker_pos_var = NULL,
  marker_shape_var = NULL,
  marker_shape_opt = NULL,
  marker_color_var = NULL,
  marker_color_opt = NULL,
  anno_txt_var = NULL,
  vref_line = NULL,
  plot_height = c(1200L, 400L, 5000L),
  plot_width = NULL,
  pre_output = NULL,
  post_output = NULL,
  x_label = "Time from First Treatment (Day)",
  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 for markers. Use "ADSL" when no markers are plotted.

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. Subject-level numeric variable for bar length (from parentname).

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"

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. Subject-level color variable from parentname.

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. Subject-level sort variable from parentname.

marker_pos_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. Marker position variable from dataname).

marker_shape_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. Marker shape variable from dataname.

marker_shape_opt

(numeric)
Named vector mapping shape values to ggplot shapes.

marker_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. Marker color variable from dataname.

marker_color_opt

(character)
Named vector mapping color values to colors.

anno_txt_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. Subject-level annotation variables from parentname (multiple selection allowed).

vref_line

(numeric)
Vertical reference lines.

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.

x_label

(character)
Label of the x axis.

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_swimlane(
   ..., # 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

Examples 

data <- within(teal_data(), {
  library(nestcolor)
  library(dplyr)
  ADSL <- teal.data::rADSL %>%
    mutate(TRTDURD = as.integer(TRTEDTM - TRTSDTM) + 1) %>%
    filter(STRATA1 == "A" & ARMCD == "ARM A")
  ADRS <- teal.data::rADRS %>%
    filter(PARAMCD == "LSTASDI" & DCSREAS == "Death") %>%
    mutate(AVALC = DCSREAS, ADY = EOSDY) %>%
    rbind(teal.data::rADRS %>% filter(PARAMCD == "OVRINV" & AVALC != "NE")) %>%
    arrange(USUBJID)
})

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


app <- init(
  data = data,
  modules = modules(
    tm_g_swimlane(
      label = "Swimlane Plot",
      dataname = "ADRS",
      bar_var = variables(
        choices = c("TRTDURD", "EOSDY"),
        selected = "TRTDURD"
      ),
      bar_color_var = variables(
        choices = c("EOSSTT", "ARM", "ARMCD", "ACTARM", "ACTARMCD", "SEX"),
        selected = "EOSSTT"
      ),
      sort_var = variables(
        choices = c("USUBJID", "SITEID", "ACTARMCD", "TRTDURD"),
        selected = "ACTARMCD"
      ),
      marker_pos_var = variables(
        choices = c("ADY"),
        selected = "ADY"
      ),
      marker_shape_var = variables(
        selected = "AVALC",
        c("AVALC", "AVISIT")
      ),
      marker_shape_opt = c("CR" = 16, "PR" = 17, "SD" = 18, "PD" = 15, "Death" = 8),
      marker_color_var = variables(
        selected = "AVALC",
        choices = c("AVALC", "AVISIT")
      ),
      marker_color_opt = c(
        "CR" = "green", "PR" = "blue", "SD" = "goldenrod",
        "PD" = "red", "Death" = "black"
      ),
      vref_line = c(30, 60),
      anno_txt_var = variables(
        selected = c("ACTARM", "SEX"),
        choices = c(
          "ARM", "ARMCD", "ACTARM", "ACTARMCD", "AGEGR1",
          "SEX", "RACE", "COUNTRY", "DCSREAS", "DCSREASP"
        )
      )
    )
  )
)
#> Initializing tm_g_swimlane
if (interactive()) {
  shinyApp(app$ui, app$server)
}