R help - Sep 2003 - coloring dendrgram in heatmap?

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

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
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help

No, I meant coloring the edges of the dendrogram on the left or top of the
image plot.


-----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
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://www.stat.math.ethz.ch/mailman/listinfo/r-help
______________________________________________
R-help at stat.math.ethz.ch mailing list
https://www.stat.math.ethz.ch/mailman/listinfo/r-help

> 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.
 
I'm not sure if this can be done with the current plot.dendrogram() (which
heatmap() calls to draw the trees).  You may want to experiment with the
edgePar argument and see if that can give you trees with different colors in
the branches.  If not, you'll need to hack into plot.dendrogram() and DIY.
(Martin would know this for sure...)

Best,
Andy
 
> -----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
> > 
> > ______________________________________________
> > R-help at stat.math.ethz.ch mailing list 
> > https://www.stat.math.ethz.ch/mailman/listinfo/r-help
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list 
> https://www.stat.math.ethz.ch/mailman/listinfo> /r-help
> 
> 
> ______________________________________________
> 
> R-help at stat.math.ethz.ch mailing list 
> https://www.stat.math.ethz.ch/mailman/listinfo> /r-help
>