After some off-line discussion I want to correct my earlier post: It's clear (even to me ;-) that the idea of reordering columns (and rows simultaneously for symmetric matrices) and then image()ing is very appropriate for correlation matrices. BTW, this has been quite an old idea, going back to Bertin (1983) and probably much longer.
What I rather meant to say was that currently heatmap() isn't setup to support this use very well. But even there I wasn't quite correct, since you can achieve quite a bit by using the `Rowv' and `Colv' arguments. Martin Maechler <[EMAIL PROTECTED]> http://stat.ethz.ch/~maechler/ Seminar fuer Statistik, ETH-Zentrum LEO C16 Leonhardstr. 27 ETH (Federal Inst. Technology) 8092 Zurich SWITZERLAND phone: x-41-1-632-3408 fax: ...-1228 <>< >>>>> "MM" == Martin Maechler <[EMAIL PROTECTED]> >>>>> on Thu, 11 Sep 2003 14:43:21 +0200 writes: >>>>> "AndyL" == Liaw, Andy <[EMAIL PROTECTED]> >>>>> on Thu, 11 Sep 2003 07:46:16 -0400 writes: AndyL> My feeling is that heatmap is not the right thing to AndyL> use on a correlation matrix. MM> definitely. AndyL> The heatmap function expects a data matrix, and does AndyL> a two-way clustering of cases and variables. It AndyL> tries to rearrange the rows and columns so that AndyL> similar colors are closer together. This obviously AndyL> will not work for a correlation matrix. (The AndyL> rearrangement is one of several enhancements that AndyL> Robert/Martin added to my original attempt.) AndyL> If you really want to do it, you may try to find my AndyL> original naive version of the heatmap function, which AndyL> I posted to the Bioconductor mailing list earlier AndyL> this year. That does not do any rearragement. MM> Thank you, Andy. MM> Further note that the upcoming version of R will also allow the MM> option of *not* doing any reordering. MM> But even then, heatmap() is not quite appropriate for MM> correlation matrices. AndyL> HTH, AndyL> Andy >>> -----Original Message----- >>> From: David Khabie-Zeitoune [mailto:[EMAIL PROTECTED] >>> Sent: Thursday, September 11, 2003 4:04 AM >>> To: [EMAIL PROTECTED] >>> Subject: [R] Flipping a heatmap >>> >>> >>> Hi >>> >>> I am using the heatmap function in package mva to look at >>> large correlation matrices visually. Is there any way to >>> "flip" the output of heatmap plot left-right so that, if >>> presented with a correlation matrix, it plots the unity >>> elements in the correlation matrix along a diagonal from top >>> left to bottom right? >>> >>> For example: >>> >>> library(mva) >>> x = matrix(rnorm(1000), ncol=10) >>> z = cor(x) >>> heatmap(z) >>> >>> Heatmap calls image, and I've found ways to do it with image e.g: >>> >>> image(z[1:10,10:1]) >>> >>> will plot things the "right" way round, but >>> >>> heatmap(z[1:10,10:1]) >>> >>> does not. >>> >>> Any help much appreciated. >>> Cheers, >>> Dave ______________________________________________ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help
