[BioC] heatmap.2 coloring question

[Srinivas Iyyer]

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
scores. 

thanks
Srini




--- "James W. MacDonald" <jmacdon at med.umich.edu>
wrote:

>  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"))
> 
> Best,
> 
> Jim
> 
> 
> 
> Srinivas Iyyer wrote:
> > Dear group, 
> > I am using heatmap.2 for heatmaps. 
> > 
> > heatmap.2(res1,cexRow = 0.28,cexCol=0.28
> >
>
,col=rev(heat.colors(16)),keysize=1,na.color=par("bg"),densadj
> > = 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
> very
> > happy if I can do that. 
> > 
> > Any suggestions, please. 
> > thank you. 
> > srini
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
>
http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 



      ____________________________________________________________________________________
Be a better friend, newshound, and