[BioC] non-symmetric heatmap colors

[Arne.Muller at sanofi-aventis.com]

Wolfgang and Sean,

thanks for your hints. The "breaks" argument (described in ?image), did what I wanted. I just had to set all fold change values < -3  to -3 and > 3 to 3 to get a saturation at these limits, otherwise the color beyond these "extreme" values would just be white.

	kind regards,

	Arne


> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Wolfgang
> Huber
> Sent: 03 February 2005 04:49
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] non-symmetric heatmap colors
> 
> 
> Hi Arne,
> 
> try the following:
> 
> library(RColorBrewer)
> library(geneplotter)
> f = colorRamp(brewer.pal(11, "RdBu"))
> 
> then f is a functions that takes numbers between 0 and 1 and maps them
> to colors between red and blue.
> 
> And
> 
> g = function(x) f( (x-x0)/(x1-x0) )
> 
> maps numbers between x0 and x1 to these colors.
> 
> Best wishes
>   Wolfgang
> 
> 
> Arne.Muller at sanofi-aventis.com wrote:
> > Hello,
> > 
> > well, it's about heatmap colors, again ... .
> > 
> > Does anybody know a package to create a non-symmetric color 
> map with user-choosen mir point and satuaration? I've a 
> fold-change matrix, with values from -3 fold (ratio 1/3) to 
> +7 fold. I'd like to go from 0.5 (green) to 1 (black) to 3 (red).
> > 
> > I think maPallete just assigns the lowest FC to the first 
> color and the highest FC to the last color, i.e. an evenly 
> distributed color list, right?
> > 
> > 	Any hints are welcome,
> > 
> > 	Arne
> 
> -------------------------------------
> Wolfgang Huber
> European Bioinformatics Institute
> European Molecular Biology Laboratory
> Cambridge CB10 1SD
> England
> Phone: +44 1223 494642
> Fax:   +44 1223 494486
> Http:  www.ebi.ac.uk/huber
> 
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