This teal module renders the UI and calls the function that creates a spaghetti plot.
Usage
tm_g_gh_spaghettiplot(
label,
dataname,
param_var,
param,
param_var_label = "PARAM",
idvar,
xaxis_var,
yaxis_var,
xaxis_var_level = NULL,
filter_var = yaxis_var,
trt_group,
trt_group_level = NULL,
group_stats = "NONE",
man_color = NULL,
color_comb = NULL,
xtick = ggplot2::waiver(),
xlabel = xtick,
rotate_xlab = FALSE,
facet_ncol = 2,
free_x = FALSE,
plot_height = c(600, 200, 2000),
plot_width = NULL,
font_size = c(12, 8, 20),
dot_size = c(2, 1, 12),
hline_arb = numeric(0),
hline_arb_color = "red",
hline_arb_label = "Horizontal line",
hline_vars = character(0),
hline_vars_colors = "green",
hline_vars_labels = hline_vars,
pre_output = NULL,
post_output = NULL
)
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.
- idvar
name of unique subject id variable.
- 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.- xaxis_var_level
vector that can be used to define the factor level of
xaxis_var
. Only use it whenxaxis_var
is character or factor.- filter_var
data constraint variable.
- 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
.- group_stats
control group mean or median overlay.
- man_color
string vector representing customized colors
- color_comb
name or hex value for combined treatment color.
- xtick
numeric vector to define the tick values of
x-axis
when x variable is numeric. Default value iswaive()
.- xlabel
vector with same length of
xtick
to define the label ofx-axis
tick values. Default value iswaive()
.- rotate_xlab
logical(1)
value indicating whether to rotatex-axis
labels- facet_ncol
numeric value indicating number of facets per row.
- free_x
logical(1)
should scales be"fixed"
(FALSE
) of"free"
(TRUE
) forx-axis
infacet_wrap
scales
parameter.- plot_height
controls plot height.
- plot_width
optional, controls plot width.
- font_size
control font size for title,
x-axis
,y-axis
and legend font.- dot_size
plot dot size.
- 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.- hline_vars
a character vector to name the columns that will define additional horizontal lines.
- hline_vars_colors
a character vector naming the colors for the additional horizontal lines.
- hline_vars_labels
a character vector naming the labels for the additional horizontal lines that will appear in the legend.
- 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.
Examples
# Example using ADaM structure analysis dataset.
data <- teal_data()
data <- within(data, {
library(dplyr)
library(stringr)
# use non-exported function from goshawk
.h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk")
# original ARM value = dose value
.arm_mapping <- list(
"A: Drug X" = "150mg QD",
"B: Placebo" = "Placebo",
"C: Combination" = "Combination"
)
set.seed(1)
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),
ANRLO = 30,
ANRHI = 75
) %>%
rowwise() %>%
group_by(PARAMCD) %>%
mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE),
paste("<", round(runif(1, min = 25, max = 30))), LBSTRESC
)) %>%
mutate(LBSTRESC = ifelse(USUBJID %in% sample(USUBJID, 1, replace = TRUE),
paste(">", round(runif(1, min = 70, max = 75))), LBSTRESC
)) %>%
ungroup()
attr(ADLB[["ARM"]], "label") <- .var_labels[["ARM"]]
attr(ADLB[["ACTARM"]], "label") <- .var_labels[["ACTARM"]]
attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"
# add LLOQ and ULOQ variables
ALB_LOQS <- .h_identify_loq_values(ADLB, "LOQFL")
ADLB <- left_join(ADLB, ALB_LOQS, by = "PARAM")
})
join_keys(data) <- default_cdisc_join_keys[names(data)]
app <- init(
data = data,
modules = modules(
tm_g_gh_spaghettiplot(
label = "Spaghetti Plot",
dataname = "ADLB",
param_var = "PARAMCD",
param = choices_selected(c("ALT", "CRP", "IGA"), "ALT"),
idvar = "USUBJID",
xaxis_var = choices_selected(c("Analysis Visit Code" = "AVISITCD"), "AVISITCD"),
yaxis_var = choices_selected(c("AVAL", "CHG", "PCHG"), "AVAL"),
filter_var = choices_selected(
c("None" = "NONE", "Screening" = "BASE2", "Baseline" = "BASE"),
"NONE"
),
trt_group = choices_selected(c("ARM", "ACTARM"), "ARM"),
color_comb = "#39ff14",
man_color = c(
"Combination" = "#000000",
"Placebo" = "#fce300",
"150mg QD" = "#5a2f5f"
),
hline_arb = c(60, 50),
hline_arb_color = c("grey", "red"),
hline_arb_label = c("default A", "default B"),
hline_vars = c("ANRHI", "ANRLO", "ULOQN", "LLOQN"),
hline_vars_colors = c("pink", "brown", "purple", "black"),
)
)
)
#> Initializing tm_g_gh_spaghettiplot
#> Initializing reporter_previewer_module
if (interactive()) {
shinyApp(app$ui, app$server)
}