Line plot
tm_g_gh_lineplot.Rd
This teal module renders the UI and calls the function that creates a line plot.
Usage
tm_g_gh_lineplot(
label,
dataname,
param_var,
param,
param_var_label = "PARAM",
xaxis_var,
yaxis_var,
xvar_level = NULL,
filter_var = yaxis_var,
filter_var_choices = filter_var,
trt_group,
trt_group_level = NULL,
shape_choices = NULL,
stat = "mean",
hline_arb = numeric(0),
hline_arb_color = "red",
hline_arb_label = "Horizontal line",
color_manual = NULL,
xtick = ggplot2::waiver(),
xlabel = xtick,
rotate_xlab = FALSE,
plot_height = c(600, 200, 4000),
plot_width = NULL,
plot_font_size = c(12, 8, 20),
dodge = c(0.4, 0, 1),
pre_output = NULL,
post_output = NULL,
count_threshold = 0,
table_font_size = c(12, 4, 20)
)
Arguments
- label
menu item label of the module in the teal app.
- dataname
analysis data passed to the data argument of teal init. E.g. ADaM structured laboratory data frame ADLB.
- param_var
name of variable containing biomarker codes e.g. PARAMCD.
- param
biomarker selected.
- param_var_label
single name of variable in analysis data that includes parameter labels.
- xaxis_var
single name of variable in analysis data that is used as x-axis in the plot for the respective goshawk function.
- yaxis_var
single name of variable in analysis data that is used as summary variable in the respective gshawk function.
- xvar_level
vector that can be used to define the factor level of xvar. Only use it when xvar is character or factor.
- filter_var
data constraint variable.
- filter_var_choices
data constraint variable choices.
- trt_group
choices_selected
object with available choices and pre-selected option for variable names representing treatment group e.g. ARM.- trt_group_level
vector that can be used to define factor level of trt_group.
- shape_choices
Vector or
choices_selected
object with names of ADSL variables which can be used to change shape- stat
string of statistics
- hline_arb
numeric vector of at most 2 values identifying intercepts for arbitrary horizontal lines.
- hline_arb_color
a character vector of at most length of
hline_arb
. naming the color for the arbitrary horizontal lines.- hline_arb_label
a character vector of at most length of
hline_arb
. naming the label for the arbitrary horizontal lines.- color_manual
string vector representing customized colors
- xtick
numeric vector to define the tick values of x-axis when x variable is numeric. Default value is waive().
- xlabel
vector with same length of xtick to define the label of x-axis tick values. Default value is waive().
- rotate_xlab
boolean value indicating whether to rotate x-axis labels.
- plot_height
controls plot height.
- plot_width
optional, controls plot width.
- plot_font_size
control font size for title, x-axis, y-axis and legend font.
- dodge
controls the position dodge of error bar
- 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 theshiny::helpText()
elements are useful.- count_threshold
minimum count of observations (as listed in the output table) to plot nodes on the graph
- table_font_size
controls the font size of values in the table
Examples
# Example using ADaM structure analysis dataset.
library(dplyr)
library(scda)
library(stringr)
# original ARM value = dose value
arm_mapping <- list(
"A: Drug X" = "150mg QD",
"B: Placebo" = "Placebo",
"C: Combination" = "Combination"
)
ADSL <- synthetic_cdisc_data("latest")$adsl
ADLB <- synthetic_cdisc_data("latest")$adlb
var_labels <- lapply(ADLB, function(x) attributes(x)$label)
ADLB <- ADLB %>%
dplyr::mutate(
AVISITCD = dplyr::case_when(
AVISIT == "SCREENING" ~ "SCR",
AVISIT == "BASELINE" ~ "BL",
grepl("WEEK", AVISIT) ~ paste("W", stringr::str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
TRUE ~ as.character(NA)
),
AVISITCDN = dplyr::case_when(
AVISITCD == "SCR" ~ -2,
AVISITCD == "BL" ~ 0,
grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
TRUE ~ as.numeric(NA)
),
AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN),
TRTORD = dplyr::case_when(
ARMCD == "ARM C" ~ 1,
ARMCD == "ARM B" ~ 2,
ARMCD == "ARM A" ~ 3
),
ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
ARM = factor(ARM) %>% reorder(TRTORD),
ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
ACTARM = factor(ACTARM) %>% reorder(TRTORD)
)
attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
app <- teal::init(
data = cdisc_data(
adsl <- cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data(\"latest\")$adsl"),
cdisc_dataset("ADLB", ADLB,
code = [1421 chars quoted with '"'],
vars = list(ADSL = adsl, arm_mapping = arm_mapping)
),
check = TRUE
),
modules = modules(
tm_g_gh_lineplot(
label = "Line Plot",
dataname = "ADLB",
param_var = "PARAMCD",
param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
shape_choices = c("SEX", "RACE"),
xaxis_var = choices_selected("AVISITCD", "AVISITCD"),
yaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
hline_arb = c(20.5, 19.5),
hline_arb_color = c("red", "green"),
hline_arb_label = c("A", "B"),
)
)
)
#> [INFO] 2022-06-14 17:42:50.1126 pid:1172 token:[] teal.goshawk Initializing tm_g_gh_lineplot
if (FALSE) {
shinyApp(app$ui, app$server)
}