I am currently using heatmap.plus to draw heatmaps with color side bars in each side (row, and column). An example of a code to plot a heatmap for a matrix of dim 18 by 50 bellow:
m.to.plot = matrix(rnorm(n=18*50,mean=3,sd=2), nrow=18, ncol=50)
colc = rainbow(2)[c(rep(x=2,30), rep(x=1,20))]
tmp = runif(n=18, min=0,max = 1)
rowc = rgb(tmp^1.5+(1-tmp^1.5)*0.742,tmp^1.5+(1-tmp^1.5)*0.742,(1-tmp^1.5)*0.742);
heatmap.plus(m.to.plot,
scale="none",
ColSideColors=colc,
RowSideColors=rowc,
Rowv=NA, Colv=NA,
col=c("green2","red2"))
Such code produce a figure like this:
But what I really want is a two column colored side bar, an example of the 'unfinished' code and it's 'in theory' image would look like this:
m.to.plot = matrix(rnorm(n=18*50,mean=3,sd=2), nrow=18, ncol=50)
colc = rainbow(2)[c(rep(x=2,30), rep(x=1,20))]
tmp = runif(n=18, min=0,max = 1)
rowc = rgb(tmp^1.5+(1-tmp^1.5)*0.742,tmp^1.5+(1-tmp^1.5)*0.742,(1-tmp^1.5)*0.742);
tmp2 = runif(n=50, min=0,max = 1)
extra.colc = rgb(tmp^1.5+(1-tmp^1.5)*0.742,tmp^1.5+(1-tmp^1.5)*0.742,(1-tmp^1.5)*0.742);
Then I need to call heatmap.plus (or change/use another heatmap.plus) such that I can visualize two column colored sided bars in the same plot
And it'd be...
voila!
Any ideas on how to modify heatmap.plus and/or the way I call the function?
Note: the heatmap function I am using is heatmap.plus, taken from bioconductor. A copy of it below (in case someone is interested).
heatmap.plus = function (x, Rowv = NULL, Colv = if (symm) "Rowv" else NULL,
distfun = dist, hclustfun = hclust, 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, RowSideColors, cexRow = 0.2 +
1/log10(nr), cexCol = 0.2 + 1/log10(nc), labRow = NULL,
labCol = NULL, cRow=NULL, cCol=NULL, main = NULL, xlab = NULL, ylab = NULL, keep.dendro = FALSE,
verbose = getOption("verbose"), ...)
{
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))
ddr <- as.dendrogram(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 {
hcc <- hclustfun(distfun(if (symm)
x
else t(x)))
ddc <- as.dendrogram(hcc)
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) 1 else 0.05) + if (!is.null(main)) 0.2 else 0,
4)
if (!missing(ColSideColors))
{
lmat <- rbind(lmat[1, ] + 1, c(NA, 1), lmat[2, ] + 1)
lhei <- c(lhei[1], 0.125/par()$fin[2]*10, lhei[2])
}
if (!missing(RowSideColors)) {
lmat <- cbind(lmat[, 1] + 1, c(rep(NA, nrow(lmat) - 1),
1), lmat[, 2] + 1)
lwid <- c(lwid[1], 0.135/par()$fin[1]*10, 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 (!missing(RowSideColors)) {
par(mar = c(margins[1L], 0, 0, 0.5))
image(rbind(1L:nr), col = RowSideColors[rowInd], axes = FALSE)
}
if (!missing(ColSideColors)) {
par(mar = c(0.5, 0, 0, margins[2L]))
image(cbind(1L:nc), col = ColSideColors[colInd], axes = FALSE)
}
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
image(1:nc, 1:nr, x, xlim = 0.5 + c(0, nc), ylim = 0.5 +
c(0, nr), axes = FALSE, xlab = "", ylab = "", ...)
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(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 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))
}
