[BioC] heatmap.2 coloring question
James W. MacDonald
jmacdon at med.umich.edu
Fri Mar 7 15:03:48 CET 2008
Srinivas Iyyer wrote:
> Thank you ! It worked.
> apologies for not asking last time another question.
> Is it possible to recreate a GSEA's Leading edge grid
> figure in R.
> I have a matrix of values based on NES(normalized
> enrichment scores) from various GSEA runs (not just
> one run).
> I combined all runs with rows as enriched gene sets
> and columns as my gene expression studies.
> I want to re-create a figure just like what GSEA
> leading edge plots look like. I tried using heatmap
> and heatmap.2 and they are not that appropriate for
> this representation.
> Is it possible to create grid and color each cells
> with a color code based on normalized enrichment
I have no idea what a GSEA leading edge plot might be, but if you want a
grid of colors, you want the image() function (which is what the
heatplot functions use).
> --- "James W. MacDonald" <jmacdon at med.umich.edu>
>> From ?colorpanel in gplots:
>> showpanel <- function(col)
>> image(z=matrix(1:100, ncol=1), col=col,
>> xaxt="n", yaxt="n" )
>> showpanel(colorpanel(40, "blue","white","yellow"))
>> Srinivas Iyyer wrote:
>>> Dear group,
>>> I am using heatmap.2 for heatmaps.
>>> heatmap.2(res1,cexRow = 0.28,cexCol=0.28
>>> = 0.25,Colv=FALSE)
>>> I want to have a color key starting from blue to
>>> yellow through white.
>>> Say -7 is my min value and +4 is my max value.
>>> Values around 0 should be totally white.
>>> what kind of trick can do that for me. I will be
>>> happy if I can do that.
>>> Any suggestions, please.
>>> thank you.
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> Search the archives:
>> James W. MacDonald, M.S.
>> Affymetrix and cDNA Microarray Core
>> University of Michigan Cancer Center
>> 1500 E. Medical Center Drive
>> 7410 CCGC
>> Ann Arbor MI 48109
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
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