>>>>> "AndyL" == Liaw, Andy <andy_liaw at merck.com>
>>>>> on Mon, 29 Sep 2003 08:28:03 -0400 writes:
>> From: Xiao-Jun Ma [mailto:xma at arcturusag.com]
>>
>> No, I meant coloring the edges of the dendrogram on the
>> left or top of the image plot.
AndyL> I'm not sure if this can be done with the current
AndyL> plot.dendrogram() (which heatmap() calls to draw the
AndyL> trees). You may want to experiment with the edgePar
AndyL> argument and see if that can give you trees with
AndyL> different colors in the branches. If not, you'll
AndyL> need to hack into plot.dendrogram() and DIY. (Martin
AndyL> would know this for sure...)
yes, you are completely right, Andy.
To make this work with heatmap() :
1) give a *dendrogram* object as `Rowv' and `Colv' argument to heatmap()
2) When constructing these 2 dendrograms, make sure that every
node to which a non-standard edge should be drawn
has an "edgePar" attribute, a list such as list(col = "green").
I agree that "2)" is somewhat tedious at the moment, but
unfortunately we are past feature freeze for R 1.8.0
{I had quite a few more proposed additional features that didn't
make it...}
Martin Maechler <maechler at stat.math.ethz.ch> 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 <><
>> -----Original Message----- From: kjetil brinchmann
>> halvorsen To: 'R-help at stat.math.ethz.ch '; 'Martin
>> Maechler ' Sent: 9/27/03 1:24 PM Subject: Re: [R]
>> coloring dendrgram in heatmap?
>>
>> On 27 Sep 2003 at 11:56, Xiao-Jun Ma wrote:
>>
>> What about trying RColorBrewer, as mentioned in the docs
>> of heatmap. I had good results with that!
>>
>> Kjetil Halvorsen
>>
>> > Using the heatmap function in mva, it seems to be hard
>> to use different > colors in the edges leading to
>> different groups of objects, as commonly done > in many
>> heatmaps in the microarray graphics. Any suggestions?
>> Thanks.
>> >
>> > max
>> >