teal.modules.clinical (version 0.9.0)

tm_g_lineplot: teal Module: Line Plot

Description

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

Usage

tm_g_lineplot(
  label,
  dataname,
  parentname = ifelse(inherits(strata, "data_extract_spec"),
    teal.transform::datanames_input(strata), "ADSL"),
  strata = teal.transform::choices_selected(teal.transform::variable_choices(parentname,
    c("ARM", "ARMCD", "ACTARMCD")), "ARM"),
  x = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    "AVISIT"), "AVISIT", fixed = TRUE),
  y = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    c("AVAL", "BASE", "CHG", "PCHG")), "AVAL"),
  y_unit = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    "AVALU"), "AVALU", fixed = TRUE),
  paramcd = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    "PARAMCD"), "PARAMCD", fixed = TRUE),
  param = teal.transform::choices_selected(teal.transform::value_choices(dataname,
    "PARAMCD", "PARAM"), "ALT"),
  conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =
    TRUE),
  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()
)

Value

a teal_module object.

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

(character or NA)
deprecated - group variable name.

x

(character)
x variable name.

y

(character)
y variable name.

y_unit

(character or NA)
y_unit variable name.

paramcd

(teal.transform::choices_selected())
object with all available choices and preselected option for the parameter code variable from dataname.

param

(character)
parameter to filter the data by.

conf_level

(teal.transform::choices_selected())
object with all available choices and pre-selected option for the confidence level, each within range of (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

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

mid_point_size

(integer or double)
controls the font size of the point for mid plot.

table_font_size

(integer or double)
controls the font size of values in the table.

plot_height

optional, (numeric)
a 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

optional, (numeric)
a 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

optional, (shiny.tag)
with text placed before the output to put the output into context. For example a title.

post_output

optional, (shiny.tag)
with text placed after the output to put the output into context. For example the shiny::helpText() elements are useful.

ggplot2_args

optional, (ggplot2_args)
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").

See Also

The TLG Catalog where additional example apps implementing this module can be found.

Examples

library(nestcolor)
library(dplyr)
library(forcats)

ADSL <- tmc_ex_adsl
ADLB <- tmc_ex_adlb %>% mutate(AVISIT == fct_reorder(AVISIT, AVISITN, min))

app <- init(
  data = cdisc_data(
    ADSL = ADSL,
    ADLB = ADLB,
    code = "
      ADSL <- tmc_ex_adsl
      ADLB <- tmc_ex_adlb %>% mutate(AVISIT == fct_reorder(AVISIT, AVISITN, min))
    "
  ),
  modules = modules(
    tm_g_lineplot(
      label = "Line Plot",
      dataname = "ADLB",
      strata = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
        "ARM"
      ),
      y = choices_selected(
        variable_choices(ADLB, c("AVAL", "BASE", "CHG", "PCHG")),
        "AVAL"
      ),
      param = choices_selected(
        value_choices(ADLB, "PARAMCD", "PARAM"),
        "ALT"
      )
    )
  )
)
if (interactive()) {
  shinyApp(app$ui, app$server)
}