This module produces a patient profile timeline ggplot2::ggplot()
type plot using ADaM datasets.
tm_g_pp_patient_timeline(
label,
dataname_adcm = "ADCM",
dataname_adae = "ADAE",
parentname = "ADSL",
patient_col = "USUBJID",
aeterm = NULL,
cmdecod = NULL,
aetime_start = NULL,
aetime_end = NULL,
dstime_start = NULL,
dstime_end = NULL,
aerelday_start = NULL,
aerelday_end = NULL,
dsrelday_start = NULL,
dsrelday_end = 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()
)
a teal_module
object.
(character
)
menu item label of the module in the teal app.
(character
)
name of ADCM
dataset or equivalent.
(character
)
name of ADAE
dataset or equivalent.
(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 CMDECOD
variable from dataname_adcm
.
(teal.transform::choices_selected()
)
object with
all available choices and preselected option for the ASTDTM
variable from dataname_adae
.
(teal.transform::choices_selected()
)
object with all
available choices and preselected option for the AENDTM
variable from dataname_adae
.
(teal.transform::choices_selected()
)
object with
all available choices and preselected option for the CMASTDTM
variable from dataname_adcm
.
(teal.transform::choices_selected()
)
object with all
available choices and preselected option for the CMAENDTM
variable from dataname_adcm
.
(teal.transform::choices_selected()
)
object
with all available choices and preselected option for the ASTDY
variable from dataname_adae
.
(teal.transform::choices_selected()
)
object
with all available choices and preselected option for the AENDY
variable from dataname_adae
.
(teal.transform::choices_selected()
)
object
with all available choices and preselected option for the ASTDY
variable from dataname_adcm
.
(teal.transform::choices_selected()
)
object
with all available choices and preselected option for the AENDY
variable from dataname_adcm
.
(numeric
)
numeric vector of length 3 of current, minimum and maximum font size values.
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.
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.
optional, (shiny.tag
)
with text placed before the output to put the output into context.
For example a title.
optional, (shiny.tag
)
with text placed after the output to put the output into context.
For example the shiny::helpText()
elements are useful.
optional, (ggplot2_args
)
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")
.
library(nestcolor)
library(dplyr)
library(formatters)
data <- teal_data()
data <- within(data, {
ADAE <- tmc_ex_adae
ADSL <- tmc_ex_adsl %>% filter(USUBJID %in% ADAE$USUBJID)
ADCM <- tmc_ex_adcm %>% mutate(
CMSTDY = case_when(
CMCAT == "medcl B" ~ 20,
CMCAT == "medcl C" ~ 150,
TRUE ~ 1
) %>% with_label("Study Day of Start of Medication"),
CMENDY = case_when(
CMCAT == "medcl B" ~ 700,
CMCAT == "medcl C" ~ 1000,
TRUE ~ 500
) %>% with_label("Study Day of End of Medication"),
CMASTDTM = ASTDTM,
CMAENDTM = AENDTM
)
})
adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", "ATC4")
datanames(data) <- c("ADSL", "ADAE", "ADCM")
join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADAE", "ADCM")]
join_keys(data)["ADCM", "ADCM"] <- adcm_keys
join_keys(data)["ADAE", "ADCM"] <- c("STUDYID", "USUBJID")
app <- init(
data = data,
modules = modules(
tm_g_pp_patient_timeline(
label = "Patient Timeline",
dataname_adae = "ADAE",
dataname_adcm = "ADCM",
parentname = "ADSL",
patient_col = "USUBJID",
plot_height = c(600L, 200L, 2000L),
cmdecod = choices_selected(
choices = variable_choices(data[["ADCM"]], "CMDECOD"),
selected = "CMDECOD",
),
aeterm = choices_selected(
choices = variable_choices(data[["ADAE"]], "AETERM"),
selected = c("AETERM")
),
aetime_start = choices_selected(
choices = variable_choices(data[["ADAE"]], "ASTDTM"),
selected = c("ASTDTM")
),
aetime_end = choices_selected(
choices = variable_choices(data[["ADAE"]], "AENDTM"),
selected = c("AENDTM")
),
dstime_start = choices_selected(
choices = variable_choices(data[["ADCM"]], "CMASTDTM"),
selected = c("CMASTDTM")
),
dstime_end = choices_selected(
choices = variable_choices(data[["ADCM"]], "CMAENDTM"),
selected = c("CMAENDTM")
),
aerelday_start = choices_selected(
choices = variable_choices(data[["ADAE"]], "ASTDY"),
selected = c("ASTDY")
),
aerelday_end = choices_selected(
choices = variable_choices(data[["ADAE"]], "AENDY"),
selected = c("AENDY")
),
dsrelday_start = choices_selected(
choices = variable_choices(data[["ADCM"]], "ASTDY"),
selected = c("ASTDY")
),
dsrelday_end = choices_selected(
choices = variable_choices(data[["ADCM"]], "AENDY"),
selected = c("AENDY")
)
)
)
)
if (interactive()) {
shinyApp(app$ui, app$server)
}
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