Hi Paolo,
First, I am assuming here that your subject line is incorrect, and
that
you are talking about the heatmap.2() function in gplots, not
something
that is in ggplot2.
On 10/2/2012 8:56 AM, Paolo Kunderfranco wrote:
> Dear All,
> I would like to add colours to my heatmap, for instance I have a set
> of genes, some are up-regulated and some are down-regulated
>
> example
> this is my data.matrix
>> x
> Pfdn5 11.73 1.000
> Aqp1 9.25 1.000
> Lims2 11.15 1.000
> Chrac1 1.00 13.990
> Sdhb 1.00 7.460
> Phpt1 8.28 1.000
> Dhrs7c 10.93 1.000
> Mrpl30 1.00 7.690
> Mrps35 11.15 1.000
> Mlf1 18.50 1.000
> Atp5h 9.29 1.000
>
>
> heatmap.2(x, Colv=F, Rowv=F,cexCol=0.5, main="test",
> cexRow=0.3,scale="row", col=greenred(75), key=F, trace="none")
>
>
>
> I would like to plot the first 3 labels in red and the rest in blue,
> is it possible with heatmap.2 function?
Not easily. You would have to modify the code to heatmap.2() to accept
the two color arguments, as well as calling axis() twice. The relevant
part of heatmap.2() looks like this:
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(4, iy, labels = labRow, las = 2, line = -0.5, tick = 0,
cex.axis = cexRow)
Where the two calls to axis() put the horizontal and vertical axis
labels on. In particular, the last axis() call does the row names.
The problem here is that you can only pass a single color for the axis
labels, so you will have to call axis(4, <otherstuff>) twice to do the
two different colors. So you will have to change that last call to do
just the first 3, with the col.axis argument set to "red", and then
the
remaining labels with the col.axis argument set to "blue". Something
like (untested):
axis(4, iy[1:3], labRow[1:3], las=2, line=-0.5,
tick=0,cex.axis=cexRow,
col.axis="red")
axis(4, iy[-c(1:3)], labRow[-c(1:3)], las=2, line=-0.5,
tick=0,cex.axis=cexRow, col.axis="blue")
I'll leave the rest of it up to you. You might need to google things
like 'R modify code' or some such if you don't know how to extract and
modify existing code in R.
Best,
Jim
> Thanks,
> Paolo
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
