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# checked in 26 December 2009 by J. Fox
# 2012-12-12: Fixed Boxplot.default() so that it works properly when g is numeric. J. Fox
# 2013-04-10: handles at argument properly, contribution of Steve Ellison. J. Fox
# 2013-08-19: removed loading of stats package. J. Fox
# 2016-09-30: added list, data.frame, and matrix methods, suggestion of Michael Friendly. J. Fox
# 2016-10-01: tweaked data.frame and list methods. J. Fox
# 2017-01-11: consolidate id argument
# 2017-10-03: add col and cex to id argument
# 2022-10-04: pointLabel() is now in the car package.
Boxplot <- function(y, ...){
arg.list <- list(...)
if (!is.null(arg.list$horizontal) && isTRUE(arg.list$horizontal))
stop("Boxplot does not support horizontal=TRUE")
UseMethod("Boxplot")
}
Boxplot.default <- function(y, g, id=TRUE, xlab, ylab, ...){
if (isFALSE(id)) {
id.method="none"
labels <- NULL
id.n <- 0
id.cex <- NULL
id.col <- NULL
}
else{
id <- applyDefaults(id, defaults=list(method="y", n=10, location="lr", cex=1, col=carPalette()[1]), type="id")
id.method <- match.arg(id$method, c("y", "identify", "none"))
id.n <- id$n
id.location <- id$location
labels <- if (is.null(id$labels)) seq(along = y)
else id$labels
id.cex <- id$cex
id.col <- id$col
}
if (missing(ylab))
ylab <- deparse(substitute(y))
pars <- list(...)
if (missing(g)) {
valid <- complete.cases(y, labels)
y <- y[valid]
labels <- labels[valid]
b <- boxplot(y, ylab = ylab, ...)
if (id.method == "none" | id.n == 0)
return(invisible(NULL))
else if (id.method == "identify") {
res <- identify(rep(1, length(y)), y, labels, cex=id.cex, col=id.col)
return(if (length(res) == 0) invisible(NULL) else labels[res])
}
else if (length(b$out) > 0) {
sel <- y %in% b$out
yy <- y[sel]
labs <- labels[sel]
which.low <- yy < b$stats[1, 1]
y.low <- yy[which.low]
labs.low <- labs[which.low]
if (length(y.low) > id.n) {
ord.low <- order(y.low)[1:id.n]
y.low <- y.low[ord.low]
labs.low <- labs.low[ord.low]
}
which.high <- yy > b$stats[5, 1]
y.high <- yy[which.high]
labs.high <- labs[which.high]
if (length(y.high) > id.n) {
ord.high <- order(y.high, decreasing = TRUE)[1:id.n]
y.high <- y.high[ord.high]
labs.high <- labs.high[ord.high]
}
labs <- c(labs.low, labs.high)
at <- if(!is.null(pars$at)) pars$at else 1
if (id.location == "lr") text(at, c(y.low, y.high), labs, pos = 2, xpd=TRUE, cex=id.cex, col=id.col)
else pointLabel(c(at, at), c(y.low, y.high, y.low, y.high),
c(paste0(" ", labs, " "), rep(" ", length(labs))),
xpd=TRUE, col=id.col, cex=id.cex)
return(if (length(labs) == 0) invisible(NULL) else labs)
}
else return(invisible(NULL))
}
else {
if (missing(xlab))
xlab = deparse(substitute(g))
valid <- complete.cases(y, labels, g)
y <- y[valid]
labels <- labels[valid]
g <- g[valid]
b <- boxplot(split(y, g), ylab = ylab, xlab = xlab, ...)
levels <- if (is.factor(g))
levels(g)
else sort(unique(g))
gg <- as.numeric(g)
if (id.method == "none" | id.n == 0)
return(invisible(NULL))
else if (id.method == "identify") {
res <- identify(gg, y, labels)
return(if (length(res) == 0) invisible(NULL) else labels[res])
}
else {
midx <- mean(par("usr")[1:2])
identified <- character(0)
if (length(b$out) > 0) {
groups <- unique(b$group)
for (group in groups) {
grp <- g == levels[group]
yy <- y[grp]
labs <- labels[grp]
sel <- yy %in% b$out[b$group == group]
yy <- yy[sel]
glabs <- labs[sel]
which.low <- yy < b$stats[1, group]
y.low <- yy[which.low]
labs.low <- glabs[which.low]
if (length(y.low) > id.n) {
ord.low <- order(y.low)[1:id.n]
y.low <- y.low[ord.low]
labs.low <- labs.low[ord.low]
}
which.high <- yy > b$stats[5, group]
y.high <- yy[which.high]
labs.high <- glabs[which.high]
if (length(y.high) > id.n) {
ord.high <- order(y.high, decreasing = TRUE)[1:id.n]
y.high <- y.high[ord.high]
labs.high <- labs.high[ord.high]
}
pos <- if (group < midx)
4
else 2
at <- if(!is.null(pars$at)) pars$at[group] else group
labs <- c(labs.low, labs.high)
if (id.location == "lr") text(at, c(y.low, y.high), labs, pos = pos, xpd=TRUE, col=id.col, cex=id.cex)
else pointLabel(c(at, at), c(y.low, y.high, y.low, y.high),
c(paste0(" ", labs, " "), rep(" ", length(labs))),
xpd=TRUE, col=id.col, cex=id.cex)
identified <- c(identified, c(labs.low, labs.high))
}
}
return(if (length(identified) == 0) invisible(NULL) else identified)
}
}
}
Boxplot.formula <- function(formula, data=NULL, subset, na.action=NULL, id=TRUE, xlab, ylab, ...){
# much of this function adapted from graphics:boxplot.formula
if (isFALSE(id)) {
id.method="none"
id.n <- 0
labels <- NULL
id.location <- "y"
id.col <- NULL
id.cex <- NULL
}
else{
id <- applyDefaults(id, defaults=list(method="y", n=10, location="lr", cex=1, col=carPalette()[1]), type="id")
id.method <- match.arg(id$method, c("y", "identify", "none"))
id.n <- id$n
id.location <- id$location
labels <- id$labels
id.col <- id$col
id.cex <- id$cex
}
m <- match.call(expand.dots = FALSE)
if (is.matrix(eval(m$data, parent.frame())))
m$data <- as.data.frame(data)
m$xlab <- m$ylab <- m$id <- m$... <- NULL
m$na.action <- na.action
m[[1]] <- as.name("model.frame")
mf <- eval(m, parent.frame())
mf$"(labels.)" <- if (is.null(labels)) rownames(mf) else labels
lab.var <- which(names(mf) == "(labels.)")
if (length(formula) == 3){
response <- attr(attr(mf, "terms"), "response")
if (missing(ylab)) ylab <- names(mf)[response]
if (missing(xlab)) xlab <- names(mf)[-c(response, lab.var)]
x <- mf[, -c(response, lab.var)]
if (is.data.frame(x)) x <- do.call("interaction", as.list(x))
if (length(xlab) > 1) xlab <- paste(xlab, collapse="*")
Boxplot(mf[[response]], x, id=list(method=id.method, labels=mf[[lab.var]],
n=id.n, location=id.location, col=id.col, cex=id.cex),
xlab=xlab, ylab=ylab, ...)
}
else if (length(formula) == 2){
if (missing(ylab)) ylab <- names(mf)[-lab.var]
Boxplot(mf[, -lab.var], id=list(method=id.method,
labels=mf[[lab.var]], n=id.n, location=id.location, col=id.col, cex=id.cex), ylab=ylab, ...)
}
else stop("improper Boxplot formula")
}
Boxplot.list <- function(y, xlab="", ylab="", ...){
if (is.null(names(y))) names(y) <- 1:length(y)
g <- factor(rep(names(y), sapply(y, length)), levels=names(y))
y <- do.call(c, y)
Boxplot(y, g, xlab=xlab, ylab=ylab, ...)
}
Boxplot.data.frame <- function(y, id=TRUE, ...){
if (isFALSE(id)) {
id.method="none"
id.n <- 0
labels <- NULL
id.location <- "y"
id.col <- NULL
id.cex <- NULL
}
else{
id <- applyDefaults(id, defaults=list(method="y", n=10, location="lr", labels=rownames(y), cex=1, col=carPalette()[1]), type="id")
id.method <- match.arg(id$method, c("y", "identify", "none"))
id.n <- id$n
id.location <- id$location
labels <- rep(id$labels, ncol(y))
id.col <- id$col
id.cex <- id$cex
}
Boxplot(as.list(y), id=list(method=id.method, n=id.n, location=id.location, labels=labels, cex=id.cex, col=id.col), ...)
}
Boxplot.matrix <- function(y, ...){
Boxplot(as.data.frame(y), ...)
}
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