tm_g_km {teal.modules.clinical} | R Documentation |
teal Module: Kaplan-Meier Plot
Description
This module produces a ggplot
-style Kaplan-Meier plot for data with ADaM structure.
Usage
tm_g_km(
label,
dataname,
parentname = ifelse(inherits(arm_var, "data_extract_spec"),
teal.transform::datanames_input(arm_var), "ADSL"),
arm_var,
arm_ref_comp = NULL,
paramcd,
strata_var,
facet_var,
time_unit_var =
teal.transform::choices_selected(teal.transform::variable_choices(dataname, "AVALU"),
"AVALU", fixed = TRUE),
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),
font_size = c(11L, 1L, 30),
control_annot_surv_med = control_surv_med_annot(),
control_annot_coxph = control_coxph_annot(x = 0.27, y = 0.35, w = 0.3),
legend_pos = c(0.9, 0.5),
rel_height_plot = c(80L, 0L, 100L),
plot_height = c(800L, 400L, 5000L),
plot_width = NULL,
pre_output = NULL,
post_output = NULL
)
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.
|
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.
|
facet_var |
(teal.transform::choices_selected() ) object with
all available choices and preselected option for names of variable that can be used for plot faceting.
|
time_unit_var |
(teal.transform::choices_selected() ) object
with all available choices and pre-selected option for the time unit variable.
|
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).
|
font_size |
(numeric ) numeric vector of length 3 of current, minimum and maximum font size values.
|
control_annot_surv_med |
(list ) parameters to control the position and size of the annotation table added
to the plot when annot_surv_med = TRUE , specified using the control_surv_med_annot() function. Parameter
options are: x , y , w , h , and fill . See control_surv_med_annot() for details.
|
control_annot_coxph |
(list ) parameters to control the position and size of the annotation table added
to the plot when annot_coxph = TRUE , specified using the control_coxph_annot() function. Parameter
options are: x , y , w , h , fill , and ref_lbls . See control_coxph_annot() for details.
|
legend_pos |
(numeric(2) or NULL ) vector containing x- and y-coordinates, respectively, for the legend
position relative to the KM plot area. If NULL (default), the legend is positioned in the bottom right corner of
the plot, or the middle right of the plot if needed to prevent overlapping.
|
rel_height_plot |
(proportion ) proportion of total figure height to allocate to the Kaplan-Meier plot.
Relative height of patients at risk table is then 1 - rel_height_plot . If annot_at_risk = FALSE or
as_list = TRUE , this parameter is ignored.
|
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.
|
Value
a teal_module
object.
See Also
The TLG Catalog where additional example
apps implementing this module can be found.
Examples
library(nestcolor)
ADSL <- tmc_ex_adsl
ADTTE <- tmc_ex_adtte
arm_ref_comp <- list(
ACTARMCD = list(
ref = "ARM B",
comp = c("ARM A", "ARM C")
),
ARM = list(
ref = "B: Placebo",
comp = c("A: Drug X", "C: Combination")
)
)
app <- init(
data = cdisc_data(
ADSL = ADSL,
ADTTE = ADTTE,
code = "
ADSL <- tmc_ex_adsl
ADTTE <- tmc_ex_adtte
"
),
modules = modules(
tm_g_km(
label = "Kaplan-Meier Plot",
dataname = "ADTTE",
arm_var = choices_selected(
variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
"ARM"
),
paramcd = choices_selected(
value_choices(ADTTE, "PARAMCD", "PARAM"),
"OS"
),
arm_ref_comp = arm_ref_comp,
strata_var = choices_selected(
variable_choices(ADSL, c("SEX", "BMRKR2")),
"SEX"
),
facet_var = choices_selected(
variable_choices(ADSL, c("SEX", "BMRKR2")),
NULL
)
)
)
)
if (interactive()) {
shinyApp(app$ui, app$server)
}
[Package
teal.modules.clinical version 0.9.1
Index]