Carol,
I don't know if there is some way in the heatmap.2 function to do so,
but if
you change the function a little bit it is possible. All you have to
do is
change the following term:
axis(4, iy, labels = labRow, las = 2, line = -0.5, tick = 0, cex.axis
=
cexRow)
to this one:
axis(2, iy, labels = labRow, las = 2, line = -0.5, tick = 0, cex.axis
=
cexRow)
I already inserted the corrected function in the end of the e-mail to
help
you. The problem that you will run into is that now the labels are
going to
be colliding with the dendrogram. This can be fixed by changing the
specifications of layout.
I hope this helps.
Cheers,
Artur
heatmap.2 <- function (x, Rowv = TRUE, Colv = if (symm) "Rowv" else
TRUE,
distfun = dist, hclustfun = hclust, dendrogram = c("both",
"row", "column", "none"), symm = FALSE, scale = c("none",
"row", "column"), na.rm = TRUE, revC = identical(Colv,
"Rowv"), add.expr, breaks, col = "heat.colors", colsep,
rowsep, sepcolor = "white", sepwidth = c(0.05, 0.05), cellnote,
notecex = 1, notecol = "cyan", na.color = par("bg"), trace =
c("column",
"row", "both", "none"), tracecol = "cyan", hline =
median(breaks),
vline = median(breaks), linecol = tracecol, margins = c(5,
5), ColSideColors, RowSideColors, cexRow = 0.2 + 1/log10(nr),
cexCol = 0.2 + 1/log10(nc), labRow = NULL, labCol = NULL,
key = TRUE, keysize = 1.5, density.info = c("histogram",
"density", "none"), denscol = tracecol, symkey = min(x <
0, na.rm = TRUE), densadj = 0.25, main = NULL, xlab = NULL,
ylab = NULL, lmat = NULL, lhei = NULL, lwid = NULL, ...)
{
scale01 <- function(x, low = min(x), high = max(x)) {
x <- (x - low)/(high - low)
x
}
scale <- if (symm && missing(scale))
"none"
else match.arg(scale)
dendrogram <- match.arg(dendrogram)
trace <- match.arg(trace)
density.info <- match.argdensity.info)
if (!missing(breaks) && (scale != "none"))
warning("Using scale=\"row\" or scale=\"column\" when breaks
are",
"specified can produce unpredictable results.", "Please
consider
using only one or the other.")
if ((Colv == "Rowv") && (!isTRUE(Rowv) || is.null(Rowv)))
Colv <- FALSE
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")
if (missing(cellnote))
cellnote <- matrix("", ncol = ncol(x), nrow = nrow(x))
if (!inherits(Rowv, "dendrogram")) {
if (((!isTRUE(Rowv)) || (is.null(Rowv))) && (dendrogram %in%
c("both", "row"))) {
if (is.logical(Colv) && (Colv))
dendrogram <- "column"
else dedrogram <- "none"
warning("Discrepancy: Rowv is FALSE, while dendrogram is
`",
dendrogram, "'. Omitting row dendogram.")
}
}
if (!inherits(Colv, "dendrogram")) {
if (((!isTRUE(Colv)) || (is.null(Colv))) && (dendrogram %in%
c("both", "column"))) {
if (is.logical(Rowv) && (Rowv))
dendrogram <- "row"
else dendrogram <- "none"
warning("Discrepancy: Colv is FALSE, while dendrogram is
`",
dendrogram, "'. Omitting column dendogram.")
}
}
if (inherits(Rowv, "dendrogram")) {
ddr <- Rowv
rowInd <- order.dendrogram(ddr)
}
else if (is.integer(Rowv)) {
hcr <- hclustfun(distfun(x))
ddr <- as.dendrogram(hcr)
ddr <- reorder(ddr, Rowv)
rowInd <- order.dendrogram(ddr)
if (nr != length(rowInd))
stop("row dendrogram ordering gave index of wrong length")
}
else if (isTRUE(Rowv)) {
Rowv <- rowMeans(x, na.rm = na.rm)
hcr <- hclustfun(distfun(x))
ddr <- as.dendrogram(hcr)
ddr <- reorder(ddr, Rowv)
rowInd <- order.dendrogram(ddr)
if (nr != length(rowInd))
stop("row dendrogram ordering gave index of wrong length")
}
else {
rowInd <- nr:1
}
if (inherits(Colv, "dendrogram")) {
ddc <- Colv
colInd <- order.dendrogram(ddc)
}
else if (identical(Colv, "Rowv")) {
if (nr != nc)
stop("Colv = \"Rowv\" but nrow(x) != ncol(x)")
if (exists("ddr")) {
ddc <- ddr
colInd <- order.dendrogram(ddc)
}
else colInd <- rowInd
}
else if (is.integer(Colv)) {
hcc <- hclustfun(distfun(if (symm)
x
else t(x)))
ddc <- as.dendrogram(hcc)
ddc <- reorder(ddc, Colv)
colInd <- order.dendrogram(ddc)
if (nc != length(colInd))
stop("column dendrogram ordering gave index of wrong
length")
}
else if (isTRUE(Colv)) {
Colv <- colMeans(x, na.rm = na.rm)
hcc <- hclustfun(distfun(if (symm)
x
else t(x)))
ddc <- as.dendrogram(hcc)
ddc <- reorder(ddc, Colv)
colInd <- order.dendrogram(ddc)
if (nc != length(colInd))
stop("column dendrogram ordering gave index of wrong
length")
}
else {
colInd <- 1:nc
}
x <- x[rowInd, colInd]
x.unscaled <- x
cellnote <- cellnote[rowInd, colInd]
if (is.null(labRow))
labRow <- if (is.null(rownames(x)))
(1:nr)[rowInd]
else rownames(x)
else labRow <- labRow[rowInd]
if (is.null(labCol))
labCol <- if (is.null(colnames(x)))
(1:nc)[colInd]
else colnames(x)
else labCol <- 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, "/")
}
if (missing(breaks) || is.null(breaks) || length(breaks) <
1)
if (missing(col))
breaks <- 16
else breaks <- length(col) + 1
if (length(breaks) == 1) {
breaks <- seq(min(x, na.rm = na.rm), max(x, na.rm = na.rm),
length = breaks)
}
nbr <- length(breaks)
ncol <- length(breaks) - 1
if (class(col) == "function")
col <- col(ncol)
else if (is.character(col) && length(col) == 1)
col <- do.call(col, list(ncol))
min.breaks <- min(breaks)
max.breaks <- max(breaks)
x[] <- ifelse(x < min.breaks, min.breaks, x)
x[] <- ifelse(x > max.breaks, max.breaks, x)
if (missing(lhei) || is.null(lhei))
lhei <- c(keysize, 4)
if (missing(lwid) || is.null(lwid))
lwid <- c(keysize, 4)
if (missing(lmat) || is.null(lmat)) {
lmat <- rbind(4:3, 2:1)
if (!missing(ColSideColors)) {
if (!is.character(ColSideColors) || length(ColSideColors)
!=
nc)
stop("'ColSideColors' must be a character vector of
length
ncol(x)")
lmat <- rbind(lmat[1, ] + 1, c(NA, 1), lmat[2, ] +
1)
lhei <- c(lhei[1], 0.2, lhei[2])
}
if (!missing(RowSideColors)) {
if (!is.character(RowSideColors) || length(RowSideColors)
!=
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 (length(lhei) != nrow(lmat))
stop("lhei must have length = nrow(lmat) = ", nrow(lmat))
if (length(lwid) != ncol(lmat))
stop("lwid must have length = ncol(lmat) =", ncol(lmat))
op <- par(no.readonly = TRUE)
on.exit(par(op))
layout(lmat, widths = lwid, heights = lhei, respect = FALSE)
if (!missing(RowSideColors)) {
par(mar = c(margins[1], 0, 0, 0.5))
image(rbind(1:nr), col = RowSideColors[rowInd], axes = FALSE)
}
if (!missing(ColSideColors)) {
par(mar = c(0.5, 0, 0, margins[2]))
image(cbind(1:nc), col = ColSideColors[colInd], axes = FALSE)
}
par(mar = c(margins[1], 0, 0, margins[2]))
if (!symm || scale != "none") {
x <- t(x)
cellnote <- t(cellnote)
}
if (revC) {
iy <- nr:1
ddr <- rev(ddr)
x <- x[, iy]
cellnote <- cellnote[, iy]
}
else iy <- 1:nr
image(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 +
c(0, nr), axes = FALSE, xlab = "", ylab = "", col = col,
breaks = breaks, ...)
if (!invalid(na.color) & anyis.na(x))) {
mmat <- ifelseis.na(x), 1, NA)
image(1:nc, 1:nr, mmat, axes = FALSE, xlab = "", ylab = "",
col = na.color, add = TRUE)
}
axis(1, 1:nc, labels = labCol, las = 2, line = -0.5, tick = 0,
cex.axis = cexCol)
if (!is.null(xlab))
mtext(xlab, side = 1, line = margins[1] - 1.25)
axis(2, 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))
if (!missing(colsep))
for (csep in colsep) rect(xleft = csep + 0.5, ybottom = rep(0,
length(csep)), xright = csep + 0.5 + sepwidth[1],
ytop = rep(ncol(x) + 1, csep), lty = 1, lwd = 1,
col = sepcolor, border = sepcolor)
if (!missing(rowsep))
for (rsep in rowsep) rect(xleft = 0, ybottom = (ncol(x) +
1 - rsep) - 0.5, xright = nrow(x) + 1, ytop = (ncol(x) +
1 - rsep) - 0.5 - sepwidth[2], lty = 1, lwd = 1,
col = sepcolor, border = sepcolor)
min.scale <- min(breaks)
max.scale <- max(breaks)
x.scaled <- scale01(t(x), min.scale, max.scale)
if (trace %in% c("both", "column")) {
for (i in colInd) {
if (!is.null(vline)) {
vline.vals <- scale01(vline, min.scale, max.scale)
abline(v = i - 0.5 + vline.vals, col = linecol,
lty = 2)
}
xv <- rep(i, nrow(x.scaled)) + x.scaled[, i] - 0.5
xv <- c(xv[1], xv)
yv <- 1:length(xv) - 0.5
lines(x = xv, y = yv, lwd = 1, col = tracecol, type = "s")
}
}
if (trace %in% c("both", "row")) {
for (i in rowInd) {
if (!is.null(hline)) {
hline.vals <- scale01(hline, min.scale, max.scale)
abline(h = i + hline, col = linecol, lty = 2)
}
yv <- rep(i, ncol(x.scaled)) + x.scaled[i, ] - 0.5
yv <- rev(c(yv[1], yv))
xv <- length(yv):1 - 0.5
lines(x = xv, y = yv, lwd = 1, col = tracecol, type = "s")
}
}
if (!missing(cellnote))
text(x = c(row(cellnote)), y = c(col(cellnote)), labels =
c(cellnote),
col = notecol, cex = notecex)
par(mar = c(margins[1], 0, 0, 0))
if (dendrogram %in% c("both", "row")) {
plot(ddr, horiz = TRUE, axes = FALSE, yaxs = "i", leaflab =
"none")
}
else plot.new()
par(mar = c(0, 0, if (!is.null(main)) 5 else 0, margins[2]))
if (dendrogram %in% c("both", "column")) {
plot(ddc, axes = FALSE, xaxs = "i", leaflab = "none")
}
else plot.new()
if (!is.null(main))
title(main, cex.main = 1.5 * op[["cex.main"]])
if (key) {
par(mar = c(5, 4, 2, 1), cex = 0.75)
if (symkey) {
max.raw <- max(abs(x), na.rm = TRUE)
min.raw <- -max.raw
}
else {
min.raw <- min(x, na.rm = TRUE)
max.raw <- max(x, na.rm = TRUE)
}
z <- seq(min.raw, max.raw, length = length(col))
image(z = matrix(z, ncol = 1), col = col, breaks = breaks,
xaxt = "n", yaxt = "n")
par(usr = c(0, 1, 0, 1))
lv <- pretty(breaks)
xv <- scale01(as.numeric(lv), min.raw, max.raw)
axis(1, at = xv, labels = lv)
if (scale == "row")
mtext(side = 1, "Row Z-Score", line = 2)
else if (scale == "column")
mtext(side = 1, "Column Z-Score", line = 2)
else mtext(side = 1, "Value", line = 2)
if density.info == "density") {
dens <- density(x, adjust = densadj, na.rm = TRUE)
omit <- dens$x < min(breaks) | dens$x > max(breaks)
dens$x <- dens$x[-omit]
dens$y <- dens$y[-omit]
dens$x <- scale01(dens$x, min.raw, max.raw)
lines(dens$x, dens$y/max(dens$y) * 0.95, col = denscol,
lwd = 1)
axis(2, at = pretty(dens$y)/max(dens$y) * 0.95,
pretty(dens$y))
title("Color Key\nand Density Plot")
par(cex = 0.5)
mtext(side = 2, "Density", line = 2)
}
else if density.info == "histogram") {
h <- hist(x, plot = FALSE, breaks = breaks)
hx <- scale01(breaks, min.raw, max.raw)
hy <- c(h$counts, h$counts[length(h$counts)])
lines(hx, hy/max(hy) * 0.95, lwd = 1, type = "s",
col = denscol)
axis(2, at = pretty(hy)/max(hy) * 0.95, pretty(hy))
title("Color Key\nand Histogram")
par(cex = 0.5)
mtext(side = 2, "Count", line = 2)
}
else title("Color Key")
}
else plot.new()
invisible(list(rowInd = rowInd, colInd = colInd))
}
On Wed, May 28, 2008 at 11:44 AM, carol white <wht_crl@yahoo.com>
wrote:
> Hi,
> How is it possible to display the row label of a heatmap (either all
or a
> selection of labels for subclusters) at the end of a row dendrogram
branches
> using preferably, heamap.2 or heatmap?
>
> Cheers,
>
> Carol
>
>
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>
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