teal Module: Forest Survival Plot

This module produces a grid-style forest plot for time-to-event data with ADaM structure.

Usage

tm_g_forest_tte(
  label,
  dataname,
  parentname = ifelse(inherits(arm_var, "data_extract_spec"),
    teal.transform::datanames_input(arm_var), "ADSL"),
  arm_var,
  arm_ref_comp = NULL,
  subgroup_var,
  paramcd,
  strata_var,
  aval_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    "AVAL"), "AVAL", fixed = TRUE),
  cnsr_var = teal.transform::choices_selected(teal.transform::variable_choices(dataname,
    "CNSR"), "CNSR", fixed = TRUE),
  conf_level = teal.transform::choices_selected(c(0.95, 0.9, 0.8), 0.95, keep_order =
    TRUE),
  time_unit_var =
    teal.transform::choices_selected(teal.transform::variable_choices(dataname, "AVALU"),
    "AVALU", fixed = TRUE),
  fixed_symbol_size = TRUE,
  plot_height = c(500L, 200L, 2000L),
  plot_width = c(1500L, 800L, 3000L),
  rel_width_forest = c(25L, 0L, 100L),
  font_size = c(15L, 1L, 30L),
  pre_output = NULL,
  post_output = NULL,
  ggplot2_args = teal.widgets::ggplot2_args()
)

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.
arm_var: (teal.transform::choices_selected())
object with all available choices and preselected option for variable names that can be used as arm_var. It defines the grouping variable(s) in the results table. If there are two elements selected for arm_var, second variable will be nested under the first variable.
arm_ref_comp: (list) optional,
if specified it must be a named list with each element corresponding to an arm variable in ADSL and the element must be another list (possibly with delayed teal.transform::variable_choices() or delayed teal.transform::value_choices() with the elements named ref and comp that the defined the default reference and comparison arms when the arm variable is changed.
subgroup_var: (teal.transform::choices_selected())
object with all available choices and preselected option for variable names that can be used as the default subgroups.
paramcd: (teal.transform::choices_selected())
object with all available choices and preselected option for the parameter code variable from dataname.
strata_var: (teal.transform::choices_selected())
names of the variables for stratified analysis.
aval_var: (teal.transform::choices_selected())
object with all available choices and pre-selected option for the analysis variable.
cnsr_var: (teal.transform::choices_selected())
object with all available choices and preselected option for the censoring variable.
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).
time_unit_var: (teal.transform::choices_selected())
object with all available choices and pre-selected option for the time unit variable.
fixed_symbol_size: (logical)
When (TRUE), the same symbol size is used for plotting each estimate. Otherwise, the symbol size will be proportional to the sample size in each each subgroup.
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.
rel_width_forest: (proportion)
proportion of total width to allocate to the forest plot. Relative width of table is then 1 - rel_width_forest. If as_list = TRUE, this parameter is ignored.
font_size: (numeric(1))
font size.
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. 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").

Value

a teal_module object.

Examples

library(nestcolor)

ADSL <- tmc_ex_adsl
ADTTE <- tmc_ex_adtte
ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label("Race")

arm_ref_comp <- list(
  ARM = list(
    ref = "B: Placebo",
    comp = c("A: Drug X", "C: Combination")
  ),
  ARMCD = list(
    ref = "ARM B",
    comp = c("ARM A", "ARM C")
  )
)

app <- init(
  data = cdisc_data(
    ADSL = ADSL,
    ADTTE = ADTTE,
    code = "
      ADSL <- tmc_ex_adsl
      ADTTE <- tmc_ex_adtte
      ADSL$RACE <- droplevels(ADSL$RACE) %>% with_label(\"Race\")
    "
  ),
  modules = modules(
    tm_g_forest_tte(
      label = "Forest Survival",
      dataname = "ADTTE",
      arm_var = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD")),
        "ARMCD"
      ),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        value_choices(ADTTE, "PARAMCD", "PARAM"),
        "OS"
      ),
      subgroup_var = choices_selected(
        variable_choices(ADSL, names(ADSL)),
        c("BMRKR2", "SEX")
      ),
      strata_var = choices_selected(
        variable_choices(ADSL, c("STRATA1", "STRATA2")),
        "STRATA2"
      )
    )
  )
)
#> Initializing tm_g_forest_tte
if (interactive()) {
  shinyApp(app$ui, app$server)
}

Usage

Arguments

Value

See also

Examples