I have correlation values between -1 and 1 and I need to keep the sign. Jeff
-----Original Message----- From: Brad McNeney [mailto:[EMAIL PROTECTED] Sent: Mon 6/25/2007 1:01 PM To: Rosenfeld, Jeffrey Cc: Neil Shephard; [email protected] Subject: Re: [R] Re : Half of a heatmap Just for the record, LDheatmap can display any upper-triangular matrix of measures between 0 and 1, not just LD measures. Users with their own matrix should pass it as the first argument (gdat) to the function. -b -- Brad McNeney Statistics and Actuarial Science Simon Fraser University Burnaby, BC, Canada On 6/25/07, Rosenfeld, Jeffrey <[EMAIL PROTECTED]> wrote: > > 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. > > > Jeff > > > -----Original Message----- > From: Neil Shephard [mailto:[EMAIL PROTECTED] > Sent: Mon 6/25/2007 6:14 AM > To: [email protected] > Cc: Rosenfeld, Jeffrey > Subject: Re : [R] Half of a heatmap > > > 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 - [EMAIL PROTECTED] / [EMAIL PROTECTED] > Website - http://slack.ser.man.ac.uk/ > Photos - http://www.flickr.com/photos/slackline/ > > ______________________________________________ > [email protected] 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. > ______________________________________________ [email protected] 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.
