R help - Oct 2007 - cut.dendrogram and cutree

Hi!

In the example:
hc <- hclust(dist(USArrests), "ave")
dend1 <- as.dendrogram(hc)
dend2 <- cut(dend1, h=70)

Do the branches "Branch 1", "Branch 2", "Branch
2"...in dend2$upper

  str(dend2$upper)
--[dendrogram w/ 2 branches and 4 members at h = 152]
   |--[dendrogram w/ 2 branches and 2 members at h = 77.6]
   |  |--leaf "Branch 1" (h= 38.5 midpoint = 0.5, x.member = 2 )
   |  `--leaf "Branch 2" (h= 44.3 midpoint = 5.03, x.member = 14 )
   `--[dendrogram w/ 2 branches and 2 members at h = 89.2]
      |--leaf "Branch 3" (h= 44.8 midpoint = 6.8, x.member = 14 )
      `--leaf "Branch 4" (h= 54.7 midpoint = 7.65, x.member = 20 )

correspond to the classes 1, 2, 3... in dendclass, where

dendclas <- cutree(hc,h=70)

?

If they do not, how can I get a vector with the original individuals
for each branch?

Thanks

Agus

-- 
Dr. Agustin Lobo
Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
LLuis Sole Sabaris s/n
08028 Barcelona
Spain
Tel. 34 934095410
Fax. 34 934110012
email: Agustin.Lobo at ija.csic.es
http://www.ija.csic.es/gt/obster

Agus,

we use cut.tree when it makes sense to use a specific h as a global
criterion to split the tree.

In your case, you might want to access the tree using '[['. Examples
below borrow the samples you provided in your code:

1) There are two branches in your dend1. To get the left branch, you can do
> dend1.1 <- dend1[[1]]
> labels(dend1.1)
where labels function gives you all the states you have under that branch.

2) There are two big sub-branches on the right branch of brand1, to
access the right one of those two sub-branches, you can do,

dend1.2.2 <- dend1[[c(2,2)]]  # or dend1.2.2<- dend1[[2]][[2]]
lables(dend1.2.2)  ## will list you all the members.

So the branches of a dendrogram object can be accessed in a binary
tree fashion, use '1' for the tree on the left and '2' for the
tree on
the right.

hope the above helps.

yaomin

------
Yaomin Xu
Statstical Computing and Bioinformatics
The Cleveland Clinic Foundation

Thanks,

But this is not solving my problem, let me further explain by following 
the example in the help page for dendrogram:

require(graphics); require(utils)
hc <- hclust(dist(USArrests), "ave")
dend1 <- as.dendrogram(hc)
dend2 <- cut(dend1, h=70)
plot(dend2$upper,center=T)

What I want to know are the original elements in each of the final 
branches of dend2$upper (the ones labeled "Branch 1", "Branch
2" etc)
(or the branch for each of the original elements).

May be I could with dend2$lower, but can't find the way.

Agus

Yaomin Xu escribi?:
> Sorry, forget to put your email address.
> 
> ---------- Forwarded message ----------
> From: Yaomin Xu <yaomin at case.edu>
> Date: Oct 28, 2007 5:14 PM
> Subject: Re: [R] cut.dendrogram and cutree
> To: r-help at r-project.org
> 
> 
> Agus,
> 
> we use cut.tree when it makes sense to use a specific h as a global
> criterion to split the tree.
> 
> In your case, you might want to access the tree using '[['.
Examples
> below borrow the samples you provided in your code:
> 
> 1) There are two branches in your dend1. To get the left branch, you can do
> 
>> dend1.1 <- dend1[[1]]
>> labels(dend1.1)
> 
> where labels function gives you all the states you have under that branch.
> 
> 2) There are two big sub-branches on the right branch of brand1, to
> access the right one of those two sub-branches, you can do,
> 
> dend1.2.2 <- dend1[[c(2,2)]]  # or dend1.2.2<- dend1[[2]][[2]]
> lables(dend1.2.2)  ## will list you all the members.
> 
> So the branches of a dendrogram object can be accessed in a binary
> tree fashion, use '1' for the tree on the left and '2' for
the tree on
> the right.
> 
> hope the above helps.
> 
> yaomin
> 
> ------
> Yaomin Xu
> Statstical Computing and Bioinformatics
> The Cleveland Clinic Foundation
> 
> 
-- 
Dr. Agustin Lobo
Institut de Ciencies de la Terra "Jaume Almera" (CSIC)
LLuis Sole Sabaris s/n
08028 Barcelona
Spain
Tel. 34 934095410
Fax. 34 934110012
email: Agustin.Lobo at ija.csic.es
http://www.ija.csic.es/gt/obster