Re: [R] Asymmetric colors for heatmap

From: <Christian.Stratowa_at_vie.boehringer-ingelheim.com>
Date: Wed 27 Jul 2005 - 22:06:39 EST


Dear Sean  

Thank you, however the heatmap() function from the stats package does not have this option.
Browsing around I see that you mean heatmap.2() from package gplots, which we have not
installed yet.  

Is there also another possibility besides heatmap.2() since I would also need this option for
e.g. function image().  

Best regards
Christian  

-----Original Message-----
From: Sean Davis [mailto:sdavis2@mail.nih.gov] Sent: Wednesday, July 27, 2005 13:16
To: Christian.Stratowa@vie.boehringer-ingelheim.com; r-help@stat.math.ethz.ch
Subject: Re: [R] Asymmetric colors for heatmap

See the breaks argument to heatmap.  

Sean

> Dear expeRts,
>
> Currently, my colors are as follows:
> mycol <-
> c("blue1","blue2","blue3","blue4","black","yellow4","yellow3","yellow2","y

> ellow1")
> 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
> heatmap.
> 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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