Stacked plot

plot.stacked.2.R

#plot.stacked makes a stacked plot where each y series is plotted on top
#of the each other using filled polygons
#
#Arguments include:
#'x' - a vector of values
#'y' - a matrix of data series (columns) corresponding to x
#'order.method' = c("as.is", "max", "first") 
#  "as.is" - plot in order of y column
#  "max" - plot in order of when each y series reaches maximum value
#  "first" - plot in order of when each y series first value > 0
#'col' - fill colors for polygons corresponding to y columns (will recycle)
#'border' - border colors for polygons corresponding to y columns (will recycle) (see ?polygon for details)
#'lwd' - border line width for polygons corresponding to y columns (will recycle)
#'...' - other plot arguments

plot.stacked <- function(
	x, y, 
	order.method = "as.is",
	ylab="", xlab="", 
	border = NULL, lwd=1, 
	col=rainbow(length(y[1,])),
	ylim=NULL,
	...
){

	if(sum(y < 0) > 0) error("y cannot contain negative numbers")

	if(is.null(border)) border <- par("fg")
	border <- as.vector(matrix(border, nrow=ncol(y), ncol=1))
	col <- as.vector(matrix(col, nrow=ncol(y), ncol=1))
	lwd <- as.vector(matrix(lwd, nrow=ncol(y), ncol=1))

	if(order.method == "max") {
		ord <- order(apply(y, 2, which.max))
		y <- y[, ord]
		col <- col[ord]
		border <- border[ord]
	}

	if(order.method == "first") {
		ord <- order(apply(y, 2, function(x) min(which(x>0))))
		y <- y[, ord]
		col <- col[ord]
		border <- border[ord]
	}

	top.old <- x*0
	polys <- vector(mode="list", ncol(y))
	for(i in seq(polys)){
		top.new <- top.old + y[,i]
		polys[[i]] <- list(x=c(x, rev(x)), y=c(top.old, rev(top.new)))
		top.old <- top.new
	}

	if(is.null(ylim)) ylim <- range(sapply(polys, function(x) range(x$y, na.rm=TRUE)), na.rm=TRUE)
	plot(x,y[,1], ylab=ylab, xlab=xlab, ylim=ylim, t="n", ...)
	for(i in seq(polys)){
		polygon(polys[[i]], border=border[i], col=col[i], lwd=lwd[i])
	}

}

Replaced top.old <- x*0 by top.old <- rep(0,length(x)) to enable time series (Posix) compatibility.
Also I'm not sure why you don't allow negative numbers here : if(sum(y < 0) > 0) error("y cannot contain negative numbers"). I personnaly use negative Y's and it works.
Thank you for this simple and efficient function !