heatmap.plus = function (x, Rowv = NULL, Colv = if (symm) "Rowv" else NULL,
distfun = dist, metric = "euclidean", distres = NULL, hclustfun = agnes, method = "ward", reorderfun = function(d,
w) reorder(d, w), add.expr, symm = FALSE, revC = identical(Colv,
"Rowv"), scale = c("row", "column", "none"), na.rm = TRUE,
margins = c(5, 5), ColSideColors = NULL, RowSideColors = NULL, cexRow = 0.2 +
1/log10(nr), cexCol = 0.2 + 1/log10(nc), labRow = NULL,
labCol = NULL, main = NULL, xlab = NULL, ylab = NULL, keep.dendro = FALSE, heatmapCol = NULL,
verbose = getOption("verbose"), legend.args = NULL,breaks=NULL, ...)
{
scale <- if (symm && missing(scale))
"none"
else match.arg(scale)
if (length(di <- dim(x)) != 2 || !is.numeric(x))
stop("'x' must be a numeric matrix")
nr <- di[1]
nc <- di[2]
if (nr <= 1 || nc <= 1)
stop("'x' must have at least 2 rows and 2 columns")
if (!is.numeric(margins) || length(margins) != 2)
stop("'margins' must be a numeric vector of length 2")
doRdend <- !identical(Rowv, NA)
doCdend <- !identical(Colv, NA)
if (is.null(Rowv))
Rowv <- rowMeans(x, na.rm = na.rm)
if (is.null(Colv))
Colv <- colMeans(x, na.rm = na.rm)
if (doRdend) {
if (inherits(Rowv, "dendrogram"))
ddr <- Rowv
else {
hcr <- hclustfun(distfun(x, method = metric), method = method)
ddr <- as.dendrogram(as.hclust(hcr))
if (!is.logical(Rowv) || Rowv)
ddr <- reorderfun(ddr, Rowv)
}
if (nr != length(rowInd <- order.dendrogram(ddr)))
stop("row dendrogram ordering gave index of wrong length")
}
else rowInd <- 1:nr
if (doCdend) {
if (inherits(Colv, "dendrogram"))
ddc <- Colv
else if (identical(Colv, "Rowv")) {
if (nr != nc)
stop("Colv = \"Rowv\" but nrow(x) != ncol(x)")
ddc <- ddr
}
else {
distRes <- if (is.null(distres)) distfun(if (symm) x else t(x), method = metric) else distres
hcc <- hclustfun(distRes, method = method)
ddc <- as.dendrogram(as.hclust(hcc), method = method)
if (!is.logical(Colv) || Colv)
ddc <- reorderfun(ddc, Colv)
}
if (nc != length(colInd <- order.dendrogram(ddc)))
stop("column dendrogram ordering gave index of wrong length")
}
else colInd <- 1:nc
x <- x[rowInd, colInd]
labRow <- if (is.null(labRow))
if (is.null(rownames(x)))
(1:nr)[rowInd]
else rownames(x)
else labRow[rowInd]
labCol <- if (is.null(labCol))
if (is.null(colnames(x)))
(1:nc)[colInd]
else colnames(x)
else labCol[colInd]
if (scale == "row") {
x <- sweep(x, 1, rowMeans(x, na.rm = na.rm))
sx <- apply(x, 1, sd, na.rm = na.rm)
x <- sweep(x, 1, sx, "/")
}
else if (scale == "column") {
x <- sweep(x, 2, colMeans(x, na.rm = na.rm))
sx <- apply(x, 2, sd, na.rm = na.rm)
x <- sweep(x, 2, sx, "/")
}
lmat <- rbind(c(NA, 3), 2:1)
lwid <- c(if (doRdend) 1 else 0.05, 4)
lhei <- c((if (doCdend) 2.5 else 0.05) + if (!is.null(main)) 0.4 else 0, 4)
#lhei <- c((if (doCdend) 1 else ) + if (!is.null(main)) 0.2 else 0, 4)
if (!is.null(ColSideColors)) {
if (!is.matrix(ColSideColors))
stop("'ColSideColors' must be a matrix")
if (!is.character(ColSideColors) || dim(ColSideColors)[1] !=
nc)
stop("'ColSideColors' dim()[2] must be of length ncol(x)")
lmat <- rbind(lmat[1, ] + 1, c(NA, 1), lmat[2, ] + 1)
#lhei <- c(lhei[1], 0.2, lhei[2])
lhei <- c(lhei[1], if (doCdend) 1.4 else 1.3, lhei[2]) #lhei <- c(lhei[1], if (doCdend) 1.4 else 1, lhei[2])
#lhei <- c(lhei[1], if (doCdend) 0.6 else 0.4, lhei[2])
}
if (!is.null(RowSideColors)) {
if (!is.matrix(RowSideColors))
stop("'RowSideColors' must be a matrix")
if (!is.character(RowSideColors) || dim(RowSideColors)[1] !=
nr)
stop("'RowSideColors' must be a character vector of length nrow(x)")
lmat <- cbind(lmat[, 1] + 1, c(rep(NA, nrow(lmat) - 1),
1), lmat[, 2] + 1)
lwid <- c(lwid[1], 0.2, lwid[2])
}
lmat[is.na(lmat)] <- 0
if (verbose) {
cat("layout: widths = ", lwid, ", heights = ", lhei,
"; lmat=\n")
#print(lmat)
}
op <- par(no.readonly = TRUE)
on.exit(par(op))
layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
if (!is.null(RowSideColors)) {
par(mar = c(margins[1], 0, 0, 0.5))
rsc = RowSideColors[rowInd, ]
rsc.colors = matrix()
rsc.names = names(table(rsc))
rsc.i = 1
for (rsc.name in rsc.names) {
rsc.colors[rsc.i] = rsc.name
rsc[rsc == rsc.name] = rsc.i
rsc.i = rsc.i + 1
}
rsc = matrix(as.numeric(rsc), nrow = dim(rsc)[1])
image(t(rsc), col = as.vector(rsc.colors), axes = FALSE)
if (ncol(RowSideColors) > 0) {
axis(1, 0:(dim(rsc)[2] - 1)/(dim(rsc)[2] - 1), colnames(RowSideColors),
las = 2, tick = FALSE)
}
}
if (!is.null(ColSideColors)) {
par(mar = c(0.5, 0, 0, margins[2]))
csc = ColSideColors[colInd, ]
csc.colors = matrix()
csc.names = names(table(csc))
csc.i = 1
for (csc.name in csc.names) {
csc.colors[csc.i] = csc.name
csc[csc == csc.name] = csc.i
csc.i = csc.i + 1
}
csc = matrix(as.numeric(csc), nrow = dim(csc)[1])
image(csc, col = as.vector(csc.colors), axes = FALSE)
if (ncol(ColSideColors) > 0) {
axis(4, 0:(dim(csc)[2] - 1)/(dim(csc)[2] - 1), colnames(ColSideColors),
las = 2, tick = FALSE, cex.axis = cexCol)
}
}
par(mar = c(margins[1], 0, 0, margins[2]))
if (!symm || scale != "none") {
x <- t(x)
}
if (revC) {
iy <- nr:1
ddr <- rev(ddr)
x <- x[, iy]
}
else iy <- 1:nr
if (is.null(breaks)) {
## add color breaks, extend the number of colorsd between the 25th and 75th quantiles
rm <- range(x)
qq1 <- quantile(unlist(x),0.25)
if (qq1 == rm[1])
qq1 <- quantile(unlist(x),0.35)
qq2 <- quantile(unlist(x),0.75)
nbCol <- length(heatmapCol)
extrNbCol <- floor(nbCol/4)-1
midNbCol <- floor(nbCol/2)
breaks <- c(seq(from = rm[1], to = qq1, by = abs(qq1-rm[1])/extrNbCol),
seq(from = qq1, to = qq2, by = (qq2-qq1)/midNbCol),
seq(from = qq2, to = rm[2], by = (rm[2]-qq2)/extrNbCol))
image(x = 1:nc, y = 1:nr, z = x, xlim = 0.5 + c(0, nc), ylim = 0.5 +
c(0, nr), axes = FALSE, xlab = "", ylab = "",
col = if (!is.null(heatmapCol)) heatmapCol else heat.colors(12),
breaks = breaks, ...)
}
else {
image(x = 1:nc, y = 1:nr, z = x, xlim = 0.5 + c(0, nc), ylim = 0.5 +
c(0, nr), axes = FALSE, xlab = "", ylab = "",
col = if (!is.null(heatmapCol)) heatmapCol else heat.colors(12),
breaks = breaks, ...) ## add colors
}
axis(1, 1:nc, labels = labCol, las = 2, line = -0.5, tick = 0,
cex.axis = cexCol)
#to have legend with bold font
opbold = par(font = 2)
if (!is.null(legend.args)) do.call(what = "legend", legend.args)
par(opbold)
if (!is.null(xlab))
mtext(xlab, side = 1, line = margins[1] - 1.25)
axis(4, iy, labels = labRow, las = 2, line = -0.5, tick = 0,
cex.axis = cexRow)
if (!is.null(ylab))
mtext(ylab, side = 4, line = margins[2] - 1.25)
if (!missing(add.expr))
eval(substitute(add.expr))
par(mar = c(margins[1], 0, 0, 0))
if (doRdend)
plot(ddr, horiz = TRUE, axes = FALSE, yaxs = "i", leaflab = "none")
else frame()
par(mar = c(0, 0, if (!is.null(main)) 1.3 else 0, margins[2]))
if (doCdend)
plot(ddc, axes = FALSE, xaxs = "i", leaflab = "none")
else if (!is.null(main))
frame()
if (!is.null(main))
title(main, cex.main = 1.5 * op[["cex.main"]])
invisible(list(rowInd = rowInd, colInd = colInd, Rowv = if (keep.dendro &&
doRdend) ddr, Colv = if (keep.dendro && doCdend) ddc))
return(list(x=x,breaks=breaks))
}
