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 > scores. 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). Best, Jim > > 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 > > _______________________________________________ > 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