R help - Sep 2011 - help with hclust and cutree

Hello,

I would like to cut a hclust tree into several groups at a specific
similarity. I assume this can be achieved by specifying the "h"
argument
with the specified similarity, e.g.:

clust<-hclust(dist,"average")
cut<-cutree(clust,h=0.65)

Now, I would like to draw rectangles around the branches of the
dendrogram highlighting the corresponding clusters, as is done by the
function rect.hclust(). How can I achieve this with the ouput of cutree?

I would appreciate your help!

Best regards,
Madeleine

plot(clust)
rect.hclust(clust, h = 0.65)

Is that what you wanted?


----- Original Message -----
From: Madeleine Seeland <madeleine.seeland at in.tum.de>
To: r-help at r-project.org
Cc: 
Sent: Tuesday, September 13, 2011 9:25 AM
Subject: [R] help with hclust and cutree

Hello,

I would like to cut a hclust tree into several groups at a specific
similarity. I assume this can be achieved by specifying the "h"
argument
with the specified similarity, e.g.:

clust<-hclust(dist,"average")
cut<-cutree(clust,h=0.65)

Now, I would like to draw rectangles around the branches of the
dendrogram highlighting the corresponding clusters, as is done by the
function rect.hclust(). How can I achieve this with the ouput of cutree?

I would appreciate your help!

Best regards,
Madeleine

______________________________________________
R-help at r-project.org 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.

Hello, 

yes, thanks!

Also,how do I get the cutoff similarity value which was used for
clustering when I cut the tree at a specific heigt?

Best regards,
Madeleine

On Tue, 2011-09-13 at 09:39 -0700, Mikkel Grum wrote:
> plot(clust)
> rect.hclust(clust, h = 0.65)
> 
> 
> 
> ----- Original Message -----
> From: Madeleine Seeland <madeleine.seeland at in.tum.de>
> To: r-help at r-project.org
> Cc: 
> Sent: Tuesday, September 13, 2011 9:25 AM
> Subject: [R] help with hclust and cutree
> 
> Hello,
> 
> I would like to cut a hclust tree into several groups at a specific
> similarity. I assume this can be achieved by specifying the
"h" argument
> with the specified similarity, e.g.:
> 
> clust<-hclust(dist,"average")
> cut<-cutree(clust,h=0.65)
> 
> Now, I would like to draw rectangles around the branches of the
> dendrogram highlighting the corresponding clusters, as is done by the
> function rect.hclust(). How can I achieve this with the ouput of cutree?
> 
> I would appreciate your help!
> 
> Best regards,
> Madeleine
> 
> ______________________________________________
> R-help at r-project.org 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.
> 

-- 
Dipl.-Wirt.-Inf. Madeleine Seeland

Technische Universit?t M?nchen
Institut f?r Informatik Lehrstuhl I12 - Bioinformatik
Boltzmannstr. 3
85748 Garching b. M?nchen, Germany

Room: MI 01.09.040 Phone: +49 (89) 289-19443 
Email: madeleine.seeland at in.tum.de
Web: http://wwwkramer.in.tum.de/people/seeland