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Hartmut Scheel | 16 May 17:49

heatmap.2 - centering the color ramp


Hello,
a short question. How would one manage to have the color range centred
around 0 instead of assigning the extreme colors (say red and green) to
the lowest and largest value? Black should be at "0" and not at the mean
value between the largest and the smallest value. I need to compare
different heatmaps.

Thanks for any suggestion
Hartmut

Here some simple Data:
mdat <-
matrix(c(1.09761079662642,0.552868871011303,0.236339539168374,-0.1568201
09742826,0.0908534304511135,-0.500217879852688,-0.182786075741673,-0.248
107861595691,-0.362157939675895),ncol=3,nrow=3,dimnames=list(c("C1","C2"
,"C3"),c("T1","T2","T3")))

 heatmap.2(mdat,Rowv=NULL,Colv="Rowv",
scale="none",col=greenred(75),key=TRUE, symkey=FALSE,
density.info="none", trace="none",dendrogram="none")

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Artur Veloso | 16 May 18:01

Re: heatmap.2 - centering the color ramp

Dear Hartmut,

Does breaks do what you need?

heatmap.2(mdat,Rowv=NULL,Colv="Rowv",
scale="none",col=greenred(75),key=TRUE, symkey=FALSE,
density.info="none", trace="none",dendrogram="none"
,breaks=seq(-1,1,length.out=76))

Cheers,

Artur

On Fri, May 16, 2008 at 11:51 AM, Hartmut Scheel <Hartmut@...>
wrote:

>
> Hello,
> a short question. How would one manage to have the color range centred
> around 0 instead of assigning the extreme colors (say red and green) to
> the lowest and largest value? Black should be at "0" and not at the mean
> value between the largest and the smallest value. I need to compare
> different heatmaps.
>
> Thanks for any suggestion
> Hartmut
>
> Here some simple Data:
> mdat <-
> matrix(c(1.09761079662642,0.552868871011303,0.236339539168374,-0.1568201
(Continue reading)

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Kauer Maximilian Otto | 19 May 13:32

Re: heatmap.2 - centering the color ramp


Hi,
the way I do that is with the heatmapCol function of the SLmisc package.
cheers,
max

-----Ursprüngliche Nachricht-----
Von: bioconductor-bounces@... im Auftrag von
Hartmut Scheel
Gesendet: Fr 16.05.2008 17:51
An: bioconductor@...
Betreff: [BioC] heatmap.2 - centering the color ramp

Hello,
a short question. How would one manage to have the color range centred
around 0 instead of assigning the extreme colors (say red and green) to
the lowest and largest value? Black should be at "0" and not at the mean
value between the largest and the smallest value. I need to compare
different heatmaps.

Thanks for any suggestion
Hartmut

Here some simple Data:
mdat <-
matrix(c(1.09761079662642,0.552868871011303,0.236339539168374,-0.1568201
09742826,0.0908534304511135,-0.500217879852688,-0.182786075741673,-0.248
107861595691,-0.362157939675895),ncol=3,nrow=3,dimnames=list(c("C1","C2"
,"C3"),c("T1","T2","T3")))
(Continue reading)

Permalink | Reply |

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