[BioC] Asymmetric colors for heatmap

Christian.Stratowa@vie.boehringer-ingelheim.com Christian.Stratowa at vie.boehringer-ingelheim.com
Tue Jul 26 09:04:31 CEST 2005

Dear all,

Currently, my colors are as follows:
mycol <-
heatmap(snp, Rowv=NA, Colv=NA, col=mycol)

However, I would like to have the following colors:
bright blue -> dark blue: for intensity range from 0 to 2 in  steps of 0.5
(i.e. 4 grades of blue)
black:  for intensity 2
dark yellow -> bright yellow: for intensity range from 2 to 8 in steps of
0.5 (i.e. 8 grades of yellow)

You may realize that I want to display copy number data from SNP-chips as
Since copynumber = 2, is the default value, I want to display it in black,
LOH in increasing blue, and amplifications in increasing yellow.
Even though there may be higher amplification rates, a value of CN=8 should
already display the brightest yellow.

In Spotfire it is easy to achieve this, especially that CN=2 is always
displayed as black, however, I do not know how to do it in R.
Can you tell me how I have to create the colors to achieve this?

(P.S.: Of course, I could do: snp[snp>8] <- 8, but this will not solve my
problem with asymmetric colors)

Thank you in advance
Christian Stratowa

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