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 <thomas.girke@ucr.edu> 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
> > Bioc-sig-sequencing@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >
>

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