From: Rosenfeld, Jeffrey <rosenfel_at_cshl.edu>

Date: Mon, 25 Jun 2007 08:20:38 -0400

Date: Mon, 25 Jun 2007 08:20:38 -0400

Thank you for your reply. I have looked at LDheatmap, but it does not seem to do what I want and seems to only work well for LD data. I was looking for something that would produce a figure identical to what heatmap.2 gives me, including the proper X and Y-axis labels and a dendogram, except that it would only have half of the map. Preferably, it would have the Color Key in the place where the other triangle of the heatmap would be, to save space.

> I am trying to produce a heatmap of pairwise correlations, but since the matrix is

*> symmetric, I only need either the upper or the lower triangle. I have scoured the
**> web and R documentation, but I have not been able to find a way to produce such a
**> figure. Is there a simple way to produce a heat map with only the part above or
**> below the diagonal?
*

You might want to check out the LDheatmap() package which can generate the plots you describe. The help indicates that it accepts a matrix of pair-wise linkage disequilibrium measures, one of which is R^2 (the correlation coefficient between loci), but I suspect you could simply pass it a matrix of correlation coefficents.

Hope that helps,

Neil

-- "In mathematics you don't understand things. You just get used to them." - Johann von Neumann Email - nshephard_at_gmail.com / n.shephard_at_sheffield.ac.uk Website - http://slack.ser.man.ac.uk/ Photos - http://www.flickr.com/photos/slackline/ ______________________________________________ R-help_at_stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.Received on Mon 25 Jun 2007 - 12:33:30 GMT

Archive maintained by Robert King, hosted by
the discipline of
statistics at the
University of Newcastle,
Australia.

Archive generated by hypermail 2.2.0, at Mon 25 Jun 2007 - 17:32:21 GMT.

*
Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help.
Please read the posting
guide before posting to the list.
*