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Christian.Stratowa@vie.boehringer-ingelheim.com

2005-Jul-27 07:54 UTC

[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
> 
> 
> 
> 
> 
>

Sean Davis

2005-Jul-27 11:15 UTC

head link

[R] Asymmetric colors for heatmap

[R] Asymmetric colors for heatmapSee the breaks argument to heatmap.

Sean
  ----- Original Message ----- 
  From: Christian.Stratowa@vie.boehringer-ingelheim.com 
  To: 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 
  > 
  > 
  > 
  > 
  > 
  > 

  ______________________________________________ 
  R-help@stat.math.ethz.ch mailing list 
  https://stat.ethz.ch/mailman/listinfo/r-help 
  PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html 

	[[alternative HTML version deleted]]

Christian.Stratowa@vie.boehringer-ingelheim.com

2005-Jul-27 12:06 UTC

head link

[R] Asymmetric colors for heatmap

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 
> 
> 
> 
> 
> 
> 
______________________________________________ 
R-help@stat.math.ethz.ch mailing list 
https://stat.ethz.ch/mailman/listinfo/r-help
<https://stat.ethz.ch/mailman/listinfo/r-help>  
PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
<http://www.R-project.org/posting-guide.html>  


	[[alternative HTML version deleted]]

Christian.Stratowa@vie.boehringer-ingelheim.com

2005-Jul-27 14:13 UTC

head link

[R] Asymmetric colors for heatmap

Sorry, my mistake, I did not realize that image() has breaks and that
heatmap() inherits from image().
However, I have the following problem, maybe I am doing something wrong.

I have defined:
   mycol <-
c("blue1","blue2","blue3","blue4","black","yellow4","yellow3","yellow2","yel
low1")
   breaks<-c(0,0.5,1,1.5,2,2.5,3,4,5,6)

When I call image() then the colors change slightly:
   image(t(tmp),col=mycol,axes=F)
   image(t(tmp),col=mycol,axes=F,breaks=breaks)

However, when I call heatmap():
   heatmap(tmp,Rowv=NA,Colv=NA,col=mycol)
   heatmap(tmp,Rowv=NA,Colv=NA,col=mycol,breaks=breaks)
then breaks results in half of the heatmap drawn in white!

Do you know what may be my mistake?

Best regards
Christian

-----Original Message-----
From: Stratowa,Dr.,Christian FEX BIG-AT-V
Sent: Wednesday, July 27, 2005 14:07
To: 'Sean Davis'; r-help at stat.math.ethz.ch
Subject: RE: [R] Asymmetric colors for heatmap


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


See the breaks argument to heatmap.

Sean

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