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 = c(getOption("ggplot2.discrete.colour"), c("#ff0000", "#008000",
"#4ca3dd", "#8a2be2"))[1:4],
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),
dot_size = c(2, 1, 12),
plot_relative_height_value = 1000
)
Arguments
- label
menu item label of the module in the teal app.
- dataname
analysis data passed to the data argument of
init
. E.g.ADaM
structured laboratory data frameADLB
.- 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
goshawk
function.- xvar_level
vector that can be used to define the factor level of
xvar
. Only use it whenxvar
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 ofADSL
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
logical(1)
value indicating whether to rotatex-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
- dot_size
plot dot size.
- plot_relative_height_value
numeric value between 500 and 5000 for controlling the starting value of the relative plot height slider
Examples
# Example using ADaM structure analysis dataset.
data <- teal_data()
data <- within(data, {
library(dplyr)
library(stringr)
library(nestcolor)
# original ARM value = dose value
arm_mapping <- list(
"A: Drug X" = "150mg QD",
"B: Placebo" = "Placebo",
"C: Combination" = "Combination"
)
ADSL <- rADSL
ADLB <- rADLB
var_labels <- lapply(ADLB, function(x) attributes(x)$label)
ADLB <- ADLB %>%
mutate(
AVISITCD = case_when(
AVISIT == "SCREENING" ~ "SCR",
AVISIT == "BASELINE" ~ "BL",
grepl("WEEK", AVISIT) ~ paste("W", str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
TRUE ~ as.character(NA)
),
AVISITCDN = case_when(
AVISITCD == "SCR" ~ -2,
AVISITCD == "BL" ~ 0,
grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
TRUE ~ as.numeric(NA)
),
AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN),
TRTORD = case_when(
ARMCD == "ARM C" ~ 1,
ARMCD == "ARM B" ~ 2,
ARMCD == "ARM A" ~ 3
),
ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
ARM = factor(ARM) %>% reorder(TRTORD),
ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
ACTARM = factor(ACTARM) %>% reorder(TRTORD)
)
attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
})
datanames <- c("ADSL", "ADLB")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]
app <- init(
data = data,
modules = modules(
tm_g_gh_lineplot(
label = "Line Plot",
dataname = "ADLB",
param_var = "PARAMCD",
param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
shape_choices = c("SEX", "RACE"),
xaxis_var = choices_selected("AVISITCD", "AVISITCD"),
yaxis_var = choices_selected(c("AVAL", "BASE", "CHG", "PCHG"), "AVAL"),
trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
hline_arb = c(20.5, 19.5),
hline_arb_color = c("red", "green"),
hline_arb_label = c("A", "B")
)
)
)
#> Initializing tm_g_gh_lineplot
#> Initializing reporter_previewer_module
if (interactive()) {
shinyApp(app$ui, app$server)
}