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

----- Original Message ----- 
From: Christian.Stratowa@vie.boehringer-ingelheim.com
<mailto:Christian.Stratowa@vie.boehringer-ingelheim.com>  
To: r-help@stat.math.ethz.ch <mailto:r-help@stat.math.ethz.ch>  
Sent: Wednesday, July 27, 2005 3:54 AM
Subject: [R] Asymmetric colors for heatmap


> 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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