teal Module: Line Plot

This module produces a ggplot2::ggplot() type line plot, with optional summary table, for standard ADaM data.

Usage

tm_g_lineplot(
  label,
  dataname,
  parentname = "ADSL",
  strata = lifecycle::deprecated(),
  group_var = teal.picks::variables(choices = c("ARM", "ARMCD", "ACTARMCD"), selected =
    "ARM"),
  x = teal.picks::variables("AVISIT", "AVISIT"),
  y = teal.picks::variables(choices = c("AVAL", "BASE", "CHG", "PCHG"), selected =
    "AVAL"),
  y_unit = teal.picks::variables("AVALU", "AVALU"),
  paramcd = teal.picks::picks(teal.picks::variables("PARAMCD", "PARAMCD", fixed = TRUE),
    teal.picks::values(c("ALT", "CRP", "IGA"), "ALT", multiple = FALSE), check_dataset =
    FALSE),
  conf_level = teal.picks::values(c(0.95, 0.9, 0.8), 0.95),
  interval = "mean_ci",
  mid = "mean",
  whiskers = c("mean_ci_lwr", "mean_ci_upr"),
  table = c("n", "mean_sd", "median", "range"),
  mid_type = "pl",
  mid_point_size = c(2, 1, 5),
  table_font_size = c(4, 2, 6),
  plot_height = c(1000L, 200L, 4000L),
  plot_width = NULL,
  pre_output = NULL,
  post_output = NULL,
  ggplot2_args = teal.widgets::ggplot2_args(),
  transformators = list(),
  decorators = list()
)

Arguments

label

(character)
menu item label of the module in the teal app.

dataname

(character)
analysis data used in teal module.

parentname

(character)
parent analysis data used in teal module, usually this refers to ADSL.

strata

Please use the group_var argument instead.

group_var, x, y, y_unit

(teal.picks::variables(), teal.picks::picks(), or legacy choices_selected)
encodings; legacy inputs are coerced with a deprecation warning.

paramcd

(teal.picks::picks() or legacy choices_selected from value_choices())
parameter code filter: a picks() chain with the PARAMCD variable and biomarker values(); defaults to ALT / CRP / IGA with ALT selected.

conf_level

(teal.picks::values(); legacy teal.transform::choices_selected() is deprecated but still accepted)
available confidence levels and default selection, each in the range (0, 1).

interval

(character or NULL)
names of the statistics that will be plotted as intervals. All the statistics indicated in interval variable must be present in the object returned by sfun, and be of a double or numeric type vector of length two. Set interval = NULL if intervals should not be added to the plot.

mid

(character or NULL)
names of the statistics that will be plotted as midpoints. All the statistics indicated in mid variable must be present in the object returned by sfun, and be of a double or numeric type vector of length one.

whiskers

(character)
names of the interval whiskers that will be plotted. Names must match names of the list element interval that will be returned by sfun (e.g. mean_ci_lwr element of sfun(x)[["mean_ci"]]). It is possible to specify one whisker only, or to suppress all whiskers by setting interval = NULL.

table

(character or NULL)
names of the statistics that will be displayed in the table below the plot. All the statistics indicated in table variable must be present in the object returned by sfun.

mid_type

(string)
controls the type of the mid plot, it can be point ("p"), line ("l"), or point and line ("pl").

mid_point_size

(numeric(1))
font size of the mid plot points.

table_font_size

(numeric(1))
font size of the text in the table.

plot_height

(numeric) optional
vector of length three with c(value, min, max). Specifies the height of the main plot and renders a slider on the plot to interactively adjust the plot height.

plot_width

(numeric) optional
vector of length three with c(value, min, max). Specifies the width of the main plot and renders a slider on the plot to interactively adjust the plot width.

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.

ggplot2_args

(ggplot2_args) optional
object created by teal.widgets::ggplot2_args() with settings for the module plot. For this module, this argument will only accept ggplot2_args object with labs list of following child elements: title, subtitle, caption, y, lty. No other elements would be taken into account. The argument is merged with option teal.ggplot2_args and with default module arguments (hard coded in the module body).

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

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.

See section "Decorating Module" below for more details.

Value

a 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_lineplot(
   ..., # arguments for module
   decorators = list(
     plot = teal_transform_module(...) # applied only to `plot` output
   )
)

For additional details and examples of decorators, refer to the vignette vignette("decorate-module-output", package = "teal.modules.clinical").

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

Examples

library(nestcolor)

data <- teal_data()
data <- within(data, {
  library(teal.modules.clinical)
  library(dplyr)
  library(forcats)
  ADSL <- tmc_ex_adsl
  ADLB <- tmc_ex_adlb %>%
    mutate(AVISIT == fct_reorder(AVISIT, AVISITN, min))
})
join_keys(data) <- default_cdisc_join_keys[names(data)]

app <- init(
  data = data,
  modules = modules(
    tm_g_lineplot(
      label = "Line Plot",
      dataname = "ADLB",
      parentname = "ADSL",
      group_var = variables(
        choices = c("ARM", "ARMCD", "ACTARMCD"),
        selected = "ARM",
        multiple = FALSE
      ),
      y = variables(
        choices = c("AVAL", "BASE", "CHG", "PCHG"),
        selected = "AVAL",
        multiple = FALSE
      ),
      paramcd = picks(
        variables("PARAMCD", fixed = TRUE),
        values(selected = "ALT", multiple = FALSE),
        check_dataset = FALSE
      )
    )
  )
)
#> Initializing tm_g_lineplot
#> Warning: rlang::dots_list(..., .ignore_empty = "trailing")
#>  - Setting explicit `selected` while `choices` are delayed (set using `tidyselect`) doesn't guarantee that `selected` is a subset of `choices`.
if (interactive()) {
  shinyApp(app$ui, app$server)
}