Thank you Thomas, That looks very nice.
Ivan Ivan Gregoretti, PhD National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health 5 Memorial Dr, Building 5, Room 205. Bethesda, MD 20892. USA. Phone: 1-301-496-1592 Fax: 1-301-496-9878 On Thu, Jun 4, 2009 at 12:00 PM, Thomas Girke <[email protected]> wrote: > Ivan, > > If I understand your problem correctly, then you could easily do this with > the heatmap or heatmap.2 functions. Below is an example how to generate > and plot such a squared overlap matrix. > > ## Some sample data set > setlist <- lapply(11:30, function(x) sample(letters, x, replace=TRUE)); > names(setlist) <- paste("S", seq(along=setlist), sep="") > > ## Compute an intersect matrix for all pairwise sample comparisons stored > in 'setlist' > olMA <- sapply(names(setlist), function(x) sapply(names(setlist), > function(y) sum(setlist[[x]] %in% setlist[[y]]))) > olMA > > ## Plot squared matrix as heat map > library("gplots") > heatmap.2(olMA, trace="none", Colv="none", Rowv="none", dendrogram="none", > col=colorpanel(40, "darkred", "orange", "yellow")) > > Here are some more examples to related problems: > > http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#R_graphics_overlapper<http://faculty.ucr.edu/%7Etgirke/Documents/R_BioCond/R_BioCondManual.html#R_graphics_overlapper> > > > T. Girke > > > > On Thu, Jun 04, 2009 at 10:56:52AM -0400, Ivan Gregoretti wrote: > > Hello everyone, > > > > How do I draw a pairwise comparison table? > > > > Simplified example of the problem: > > > > 1) lets say I have several sets of ChIP-seq peaks from several > > experiments: setA, setB, setC, etc. Many sets. > > > > 2) I know how many peaks in common are held by each pair of sets. For > > instance, setA and setB have 300 peaks in common (overlaps). I can > > create a square matrix to hold all pairwise values. > > > > 3) Now I want to draw something like a square table where both columns > > and rows are labelled setA, setB, setC, etc. In position [setA, setB] > > I would write 300 (and so I would on position [setB, setA]). > > > > Is there any R function created to address this need? Perhaps > > something like a general purpose heat map? > > > > Any pointer would be appreciated. > > > > Ivan > > > > Ivan Gregoretti, PhD > > National Institute of Diabetes and Digestive and Kidney Diseases > > National Institutes of Health > > 5 Memorial Dr, Building 5, Room 205. > > Bethesda, MD 20892. USA. > > Phone: 1-301-496-1592 > > Fax: 1-301-496-9878 > > > > _______________________________________________ > > Bioc-sig-sequencing mailing list > > [email protected] > > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
