[BioC] heatmap.2

Jenny Drnevich drnevich at uiuc.edu
Wed Aug 1 17:14:37 CEST 2007


Hi,

I prefer not to standardize around 0 or use the 
scale="row" option of heatmap2, because it's not 
always clear what the resulting values mean. What 
I've done is to add a row to the data to force the center to be on zero:

 > class(mean.sig.05)
[1] "matrix"

 > dim(mean.sig.05)
[1] 101  15

 > max(mean.sig.05)
[1] 3.24023

 > min(mean.sig.05)
[1] -3.120530

 > mean.sig.05 <- rbind(mean.sig.05,fake=c(3.24,rep(0,13),-3.24))

 > rownames(mean.sig.05) <- NULL

 >hmcol2 <- colorRampPalette(c("red","white","blue"))(256)

 > heatmap_2(mean.sig.05,col=hmcol2,legend=1,do.dendro=c(T,T),scale="none")

Of course, it's not ideal to have a faked row of 
data in the plot, but it doesn't really show if you have >50 genes.

Cheers,
Jenny

At 06:24 AM 8/1/2007, Benjamin Otto wrote:
>How about data standardization before plotting? Should center the values
>automatically around 0. There is some flag in the function to da that,
>but I don't have it in mind right now.
>
>regards,
>
>Benjamin
>
>
>Am Dienstag, den 31.07.2007, 09:56 +0200 schrieb Kauer Maximilian Otto:
> > Dear list,
> >
> > Is there a way to force the colors in 
> heatmap.2 to center on 0 i.e to to force 0 to 
> be white even though the spread in the data is 
> unequal (say -7 to +4)? I'm using bluered, but could use different color sets.
> >
> > Thank You,
> > Max
> >
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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

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