[BioC] heatmap.2 coloring question
srini_iyyer_bio at yahoo.com
Thu Mar 6 20:35:31 CET 2008
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
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
Is it possible to create grid and color each cells
with a color code based on normalized enrichment
--- "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.
> > srini
> > _______________________________________________
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> 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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