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geom_bracket.R
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#' @include utilities.R
NULL
StatBracket <- ggplot2::ggproto("StatBracket", ggplot2::Stat,
required_aes = c("x", "y", "group"),
setup_params = function(data, params) {
if(length(params$tip.length) == 1) params$tip.length <- rep(params$tip.length, max(length(params$xmin), 1) * 2)
if(length(params$tip.length) == length(params$xmin)) params$tip.length <- rep(params$tip.length, each=2)
return(params)
},
compute_group = function(data, scales, tip.length) {
yrange <- scales$y$range$range
y.scale.range <- yrange[2] - yrange[1]
bracket.shorten <- data$bracket.shorten/2
xmin <- data$xmin + bracket.shorten
xmax <- data$xmax - bracket.shorten
y.position <- data$y.position + (y.scale.range*data$step.increase) + data$bracket.nudge.y
label <- data$label
if(is.character(xmin)){
xmin <- scales$x$map(xmin)
}
if(is.character(xmax)){
xmax <- scales$x$map(xmax)
}
if("tip.length" %in% colnames(data)){
tip.length <- rep(data$tip.length, each=2)
}
# Preparing bracket data
data <- dplyr::bind_rows(data, data, data)
data$x <- c(xmin, xmin, xmax)
data$xend = c(xmin, xmax, xmax)
data$y <- c(y.position - y.scale.range*tip.length[seq_len(length(tip.length))%% 2 == 1], y.position, y.position)
data$yend <- c(y.position, y.position, y.position-y.scale.range*tip.length[seq_len(length(tip.length))%% 2 == 0])
data$annotation <- rep(label, 3)
data
}
)
#' Add Brackets with Labels to a GGPlot
#' @description add brackets with label annotation to a ggplot. Helpers for
#' adding p-value or significance levels to a plot.
#' @param label character vector with alternative label, if not null test is
#' ignored
#' @param type the label type. Can be one of "text" and "expression" (for
#' parsing plotmath expression).
#' @param xmin numeric vector with the positions of the left sides of the
#' brackets
#' @param xmax numeric vector with the positions of the right sides of the
#' brackets
#' @param y.position numeric vector with the y positions of the brackets
#' @param size change the width of the lines of the bracket
#' @param label.size change the size of the label text
#' @param family change the font used for the text
#' @param vjust move the text up or down relative to the bracket
#' @param step.increase numeric vector with the increase in fraction of total
#' height for every additional comparison to minimize overlap.
#' @param bracket.nudge.y Vertical adjustment to nudge brackets by. Useful to
#' move up or move down the bracket. If positive value, brackets will be moved
#' up; if negative value, brackets are moved down.
#' @param bracket.shorten a small numeric value in [0-1] for shortening the with
#' of bracket.
#' @param step.group.by a variable name for grouping brackets before adding
#' step.increase. Useful to group bracket by facet panel.
#' @param tip.length numeric vector with the fraction of total height that the
#' bar goes down to indicate the precise column
#' @param na.rm If \code{FALSE} (the default), removes missing values with a
#' warning. If \code{TRUE} silently removes missing values.
#' @param coord.flip logical. If \code{TRUE}, flip x and y coordinates so that
#' horizontal becomes vertical, and vertical, horizontal. When adding the
#' p-values to a horizontal ggplot (generated using
#' \code{\link[ggplot2]{coord_flip}()}), you need to specify the option
#' \code{coord.flip = TRUE}.
#' @param ... other arguments passed on to \code{\link{layer}}. These are often
#' aesthetics, used to set an aesthetic to a fixed value, like \code{color =
#' "red"} or \code{size = 3}. They may also be parameters to the paired
#' geom/stat.
#' @inheritParams ggplot2::layer
#' @examples
#' df <- ToothGrowth
#' df$dose <- factor(df$dose)
#'
#' # Add bracket with labels
#' ggboxplot(df, x = "dose", y = "len") +
#' geom_bracket(
#' xmin = "0.5", xmax = "1", y.position = 30,
#' label = "t-test, p < 0.05"
#' )
#'
#' # Customize bracket tip.length tip.length
#' ggboxplot(df, x = "dose", y = "len") +
#' geom_bracket(
#' xmin = "0.5", xmax = "1", y.position = 30,
#' label = "t-test, p < 0.05", tip.length = c(0.2, 0.02)
#' )
#'
#' #Using plotmath expression
#' ggboxplot(df, x = "dose", y = "len") +
#' geom_bracket(
#' xmin = "0.5", xmax = "1", y.position = 30,
#' label = "list(~italic(p)<=0.001)", type = "expression",
#' tip.length = c(0.2, 0.02)
#' )
#'
#' # Specify multiple brackets manually
#' ggboxplot(df, x = "dose", y = "len") +
#' geom_bracket(
#' xmin = c("0.5", "1"), xmax = c("1", "2"),
#' y.position = c(30, 35), label = c("***", "**"),
#' tip.length = 0.01
#' )
#'
#' # Compute statistical tests and add p-values
#' stat.test <- compare_means(len ~ dose, ToothGrowth, method = "t.test")
#' ggboxplot(df, x = "dose", y = "len") +
#' geom_bracket(
#' aes(xmin = group1, xmax = group2, label = signif(p, 2)),
#' data = stat.test, y.position = 35
#' )
#'
#' # Increase step length between brackets
#' ggboxplot(df, x = "dose", y = "len") +
#' geom_bracket(
#' aes(xmin = group1, xmax = group2, label = signif(p, 2)),
#' data = stat.test, y.position = 35, step.increase = 0.1
#' )
#'
#' # Or specify the positions of each comparison
#' ggboxplot(df, x = "dose", y = "len") +
#' geom_bracket(
#' aes(xmin = group1, xmax = group2, label = signif(p, 2)),
#' data = stat.test, y.position = c(32, 35, 38)
#' )
#' @rdname geom_bracket
#' @export
stat_bracket <- function(mapping = NULL, data = NULL,
position = "identity", na.rm = FALSE, show.legend = NA,
inherit.aes = TRUE,
label = NULL, type = c("text", "expression"), y.position=NULL, xmin = NULL, xmax = NULL,
step.increase = 0, step.group.by = NULL, tip.length = 0.03,
bracket.nudge.y = 0, bracket.shorten = 0,
size = 0.3, label.size = 3.88, family="", vjust = 0,
...) {
if(! is.null(data) & ! is.null(mapping)){
if(! "x" %in% names(data)) mapping$x <- 1
if(! "y" %in% names(data)) mapping$y <- 1
}
type <- match.arg(type)
ggplot2::layer(
stat = StatBracket, data = data, mapping = mapping, geom = "bracket",
position = position, show.legend = show.legend, inherit.aes = inherit.aes,
params = list(
label=label, type = type,
y.position=y.position,xmin=xmin, xmax=xmax,
step.increase=step.increase, bracket.nudge.y = bracket.nudge.y,
bracket.shorten = bracket.shorten, step.group.by = step.group.by,
tip.length=tip.length, size=size, label.size=label.size,
family=family, vjust=vjust, na.rm = na.rm, ...)
)
}
GeomBracket <- ggplot2::ggproto("GeomBracket", ggplot2::Geom,
required_aes = c("x", "xend", "y", "yend", "annotation"),
default_aes = ggplot2::aes(
shape = 19, colour = "black", label.size = 3.88, angle = NULL, hjust = 0.5,
vjust = 0, alpha = NA, family = "", fontface = 1, lineheight = 1.2, linetype=1, size = 0.3,
xmin = NULL, xmax = NULL, label = NULL, y.position = NULL, step.increase = 0,
bracket.nudge.y = 0, bracket.shorten = 0 # Added to avoid aesthetics warning
),
# draw_key = function(...){grid::nullGrob()},
# for legend:
draw_key = draw_key_path,
draw_group = function(data, panel_params, coord, type = "text",
coord.flip = FALSE) {
lab <- as.character(data$annotation)
if(type == "expression"){
lab <- parse_as_expression(lab)
}
coords <- coord$transform(data, panel_params)
label.x <- mean(c(coords$x[1], tail(coords$xend, n=1)))
label.y <- max(c(coords$y, coords$yend))+0.01
label.angle <- coords$angle
if(coord.flip){
label.y <- mean(c(coords$y[1], tail(coords$yend, n=1)))
label.x <- max(c(coords$x, coords$xend))+0.01
if(is.null(label.angle)) label.angle <- -90
}
if(is.null(label.angle)) label.angle <- 0
grid::gList(
grid::textGrob(
label = lab,
x = label.x,
y = label.y,
default.units = "native",
hjust = coords$hjust, vjust = coords$vjust,
rot = label.angle,
gp = grid::gpar(
col = scales::alpha(coords$colour, coords$alpha),
fontsize = coords$label.size * ggplot2::.pt,
fontfamily = coords$family,
fontface = coords$fontface,
lineheight = coords$lineheight
)
),
grid::segmentsGrob(
coords$x, coords$y,
default.units = "native",
coords$xend, coords$yend,
gp = grid::gpar(
col = scales::alpha(coords$colour, coords$alpha),
lty = coords$linetype,
lwd = coords$size * ggplot2::.pt
)
)
)
}
)
#' @rdname geom_bracket
#' @export
geom_bracket <- function(mapping = NULL, data = NULL, stat = "bracket",
position = "identity", na.rm = FALSE, show.legend = NA,
inherit.aes = TRUE,
label = NULL, type = c("text", "expression"), y.position = NULL, xmin = NULL, xmax = NULL,
step.increase = 0, step.group.by = NULL, tip.length = 0.03,
bracket.nudge.y = 0, bracket.shorten = 0,
size = 0.3, label.size = 3.88, family="", vjust = 0,
coord.flip = FALSE,
...) {
type <- match.arg(type)
data <- build_signif_data(
data = data, label = label, y.position = y.position,
xmin = xmin, xmax = xmax, step.increase = step.increase,
bracket.nudge.y = bracket.nudge.y, bracket.shorten = bracket.shorten,
step.group.by = step.group.by, vjust = vjust
)
mapping <- build_signif_mapping(mapping, data)
ggplot2::layer(
stat = stat, geom = GeomBracket, mapping = mapping, data = data,
position = position, show.legend = show.legend, inherit.aes = inherit.aes,
params = list(
type = type,
tip.length = tip.length,
size = size, label.size = label.size,
family = family, na.rm = na.rm, coord.flip = coord.flip,
...
)
)
}
# Guess column to be used as significance labem
guess_signif_label_column <- function(data){
potential.label <- c(
"label", "labels", "p.adj.signif", "p.adj", "padj",
"p.signif", "p.value", "pval", "p.val", "p"
)
res <- intersect(potential.label, colnames(data))
if(length(res) > 0){
res <- res[1]
}
else{
stop("label is missing")
}
res
}
build_signif_data <- function(data = NULL, label = NULL, y.position = NULL,
xmin = NULL, xmax = NULL, step.increase = 0,
bracket.nudge.y = 0, bracket.shorten = 0, step.group.by = NULL, vjust = 0){
add_step_increase <- function(data, step.increase){
comparisons.number <- 0:(nrow(data)-1)
step.increase <- step.increase*comparisons.number
data <- data %>% mutate(step.increase = !!step.increase)
data
}
if(is.null(data)){
data <- data.frame(
label = label, y.position = y.position,
xmin = xmin, xmax = xmax
) %>%
mutate(vjust = !!vjust)
}
else{
if(!is.null(label)) data <- data %>% mutate(label = !!label)
if(!is.null(y.position)) data <- data %>% mutate(y.position = !!y.position)
if(!is.null(xmin)) data <- data %>% mutate(xmin = !!xmin)
if(!is.null(xmax)) data <- data %>% mutate(xmax = !!xmax)
if(!identical(vjust, 0)) data <- data %>% mutate(vjust = !!vjust)
}
# add vjust column if doesn't exist
if(!("vjust" %in% colnames(data))) data <- data %>% mutate(vjust = !!vjust)
if(!("bracket.nudge.y" %in% colnames(data))) data <- data %>% mutate(bracket.nudge.y = !!bracket.nudge.y)
if(!("bracket.shorten" %in% colnames(data))) data <- data %>% mutate(bracket.shorten= !!bracket.shorten)
if(is.null(step.group.by)){
data <- data %>% add_step_increase(step.increase)
}
else{
data <- data %>%
dplyr::arrange(!!!syms(c(step.group.by, "y.position"))) %>%
group_by(!!!syms(step.group.by)) %>%
tidyr::nest() %>%
dplyr::mutate(step.increase = purrr::map(data, add_step_increase, !!step.increase)) %>%
dplyr::select(-data) %>%
unnest(cols = "step.increase")
}
data
}
build_signif_mapping <- function(mapping, data){
if(is.null(mapping)){
# Check if required variables are present in data
required.vars <- c("xmin", "xmax", "y.position")
missing.required.vars <- setdiff(required.vars, colnames(data))
if(length(missing.required.vars) > 0){
stop(
"Required variables are missing in the data: ",
paste(missing.required.vars, collapse = ", ")
)
}
mapping <- ggplot2::aes()
}
if(is.null(mapping$label)){
label.col <- guess_signif_label_column(data)
data$label <- data %>% dplyr::pull(!!label.col)
mapping$label <- data$label
}
if(is.null(mapping$xmin)) mapping$xmin <- data$xmin
if(is.null(mapping$xmax)) mapping$xmax <- data$xmax
if(is.null(mapping$y.position)) mapping$y.position <- data$y.position
if(is.null(mapping$group)) mapping$group <- 1:nrow(data)
if(is.null(mapping$step.increase)) mapping$step.increase <- data$step.increase
if(is.null(mapping$vjust)) mapping$vjust <- data$vjust
if(is.null(mapping$bracket.nudge.y)) mapping$bracket.nudge.y <- data$bracket.nudge.y
if(is.null(mapping$bracket.shorten)) mapping$bracket.shorten <- data$bracket.shorten
if(! "x" %in% names(mapping)){
mapping$x <- mapping$xmin
}
if(! "y" %in% names(mapping)){
mapping$y <- mapping$y.position
}
mapping
}
# Source: https://github.com/tidyverse/ggplot2/issues/2864
parse_as_expression <- function(text) {
stopifnot(is.character(text))
out <- vector("expression", length(text))
for (i in seq_along(text)) {
expr <- parse(text = text[[i]])
out[[i]] <- if (length(expr) == 0) NA else expr[[1]]
}
out
}