This module produces an adverse events table and ggplot2::ggplot()
type plot using ADaM datasets.
tm_g_pp_adverse_events(
label,
dataname = "ADAE",
parentname = "ADSL",
patient_col = "USUBJID",
aeterm = NULL,
tox_grade = NULL,
causality = NULL,
outcome = NULL,
action = NULL,
time = NULL,
decod = NULL,
font_size = c(12L, 12L, 25L),
plot_height = c(700L, 200L, 2000L),
plot_width = NULL,
pre_output = NULL,
post_output = NULL,
ggplot2_args = teal.widgets::ggplot2_args(),
transformators = list(),
decorators = list()
)
a teal_module
object.
(character
)
menu item label of the module in the teal app.
(character
)
analysis data used in teal module.
(character
)
parent analysis data used in teal module, usually this refers to ADSL
.
(character
)
name of patient ID variable.
(teal.transform::choices_selected()
)
object with all
available choices and preselected option for the AETERM
variable from dataname
.
(teal.transform::choices_selected()
)
object with all
available choices and preselected option for the AETOXGR
variable from dataname
.
(teal.transform::choices_selected()
)
object with all
available choices and preselected option for the AEREL
variable from dataname
.
(teal.transform::choices_selected()
)
object with all
available choices and preselected option for the AEOUT
variable from dataname
.
(teal.transform::choices_selected()
)
object with all
available choices and preselected option for the AEACN
variable from dataname
.
(teal.transform::choices_selected()
)
object with all
available choices and preselected option for the ASTDY
variable from dataname
.
(teal.transform::choices_selected()
)
object with all
available choices and preselected option for the AEDECOD
variable from dataname
.
(numeric
)
numeric vector of length 3 of current, minimum and maximum font size values.
(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.
(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.
(shiny.tag
) optional,
with text placed before the output to put the output into context.
For example a title.
(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
) 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")
.
(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")
.
(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.
This module generates the following objects, which can be modified in place using decorators::
plot
(ggplot
)
table
(datatables
- output of DT::datatable()
)
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_pp_adverse_events(
..., # arguments for module
decorators = list(
plot = teal_transform_module(...), # applied only to `plot` output
table = teal_transform_module(...) # applied only to `table` 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.
library(nestcolor)
library(dplyr)
data <- teal_data()
data <- within(data, {
ADAE <- tmc_ex_adae
ADSL <- tmc_ex_adsl %>%
filter(USUBJID %in% ADAE$USUBJID)
})
join_keys(data) <- default_cdisc_join_keys[names(data)]
ADSL <- data[["ADSL"]]
ADAE <- data[["ADAE"]]
app <- init(
data = data,
modules = modules(
tm_g_pp_adverse_events(
label = "Adverse Events",
dataname = "ADAE",
parentname = "ADSL",
patient_col = "USUBJID",
plot_height = c(600L, 200L, 2000L),
aeterm = choices_selected(
choices = variable_choices(ADAE, "AETERM"),
selected = "AETERM"
),
tox_grade = choices_selected(
choices = variable_choices(ADAE, "AETOXGR"),
selected = "AETOXGR"
),
causality = choices_selected(
choices = variable_choices(ADAE, "AEREL"),
selected = "AEREL"
),
outcome = choices_selected(
choices = variable_choices(ADAE, "AEOUT"),
selected = "AEOUT"
),
action = choices_selected(
choices = variable_choices(ADAE, "AEACN"),
selected = "AEACN"
),
time = choices_selected(
choices = variable_choices(ADAE, "ASTDY"),
selected = "ASTDY"
),
decod = NULL
)
)
)
if (interactive()) {
shinyApp(app$ui, app$server)
}
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