R help - Jun 2010 - plotting radial dendrograms

Dear list,

I am trying to plot a radial dendrogram using the ape package, which
requires my data to be of class 'phylo'. Currently I have my
dendrogram stored as an object of class 'dendrogram' which was
produced from an outside bit of C code, but was made into an object of
class 'igraph.eigenc' and converted to a dendrogram using
'as.dendrogram()' from the igraph package. I would like to find a way
to convert this dendrogram to a 'phylo' object, either directly, or
through conversion via 'hclust'. I have tried creating an
'hclust'
object 'manually' but keep running into "Error: segfault from C
stack
overflow" when I try to plot it:
> result <- list()
> result$merge<-merges
> result$method <- NULL
> result$dist.method <- "modularity"
> result$height <- seq(length(merges[,1]),1,-1)
> result$order <- seq(length(merges[,1])+1)
> result$call <- "some call"
> class(result) <- "hclust"
> plot(result)
where merges is a two column matrix of cluster joins that looks
something like this:
> merges
     [,1] [,2]
[1,]    0    2
[2,]    3    1

The dendrogram object was created using something like this:
> result <- list()
> class(result) <- "igraph.eigenc"
> result$merges <- merges
> result$membership <- membership
> dend <- as.dendrogram(result)
where merges is as above, and membership is:
> membership
[1] 0 0 0 0 0 2 2 2 2 2 1 1 1 1 1

Any thoughts on how to convert a dendrogram object to an hclust or
phylo object, or barring that, another way to plot a radial dendrogam
in R?

Regards,

Carson

-- 
Carson J. Q. Farmer
ISSP Doctoral Fellow
National Centre for Geocomputation
National University of Ireland, Maynooth,
http://www.carsonfarmer.com/

In which format do you get the dendrogram out of the C code? If it's
possible to get it as a newick or nexus formatted tree, you can get it
easily into R with read.tree() or read.nexus() in the ape package.
newick2phylog() from the ade4 package can be helpful as well, as you
get a phylog object and you can use the functions of the ade4 package
for plotting radial dendrograms.

Hope this helps.
Cheers
Joris

On Thu, Jun 17, 2010 at 1:50 PM, Carson Farmer <carson.farmer at
gmail.com> wrote:
> Dear list,
>
> I am trying to plot a radial dendrogram using the ape package, which
> requires my data to be of class 'phylo'. Currently I have my
> dendrogram stored as an object of class 'dendrogram' which was
> produced from an outside bit of C code, but was made into an object of
> class 'igraph.eigenc' and converted to a dendrogram using
> 'as.dendrogram()' from the igraph package. I would like to find a
way
> to convert this dendrogram to a 'phylo' object, either directly, or
> through conversion via 'hclust'. I have tried creating an
'hclust'
> object 'manually' but keep running into "Error: segfault from
C stack
> overflow" when I try to plot it:
>
>> result <- list()
>> result$merge<-merges
>> result$method <- NULL
>> result$dist.method <- "modularity"
>> result$height <- seq(length(merges[,1]),1,-1)
>> result$order <- seq(length(merges[,1])+1)
>> result$call <- "some call"
>> class(result) <- "hclust"
>> plot(result)
>
> where merges is a two column matrix of cluster joins that looks
> something like this:
>
>> merges
> ? ? [,1] [,2]
> [1,] ? ?0 ? ?2
> [2,] ? ?3 ? ?1
>
> The dendrogram object was created using something like this:
>
>> result <- list()
>> class(result) <- "igraph.eigenc"
>> result$merges <- merges
>> result$membership <- membership
>> dend <- as.dendrogram(result)
>
> where merges is as above, and membership is:
>
>> membership
> [1] 0 0 0 0 0 2 2 2 2 2 1 1 1 1 1
>
> Any thoughts on how to convert a dendrogram object to an hclust or
> phylo object, or barring that, another way to plot a radial dendrogam
> in R?
>
> Regards,
>
> Carson
>
> --
> Carson J. Q. Farmer
> ISSP Doctoral Fellow
> National Centre for Geocomputation
> National University of Ireland, Maynooth,
> http://www.carsonfarmer.com/
>
> ______________________________________________
> 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.
>


-- 
Joris Meys
Statistical consultant

Ghent University
Faculty of Bioscience Engineering
Department of Applied mathematics, biometrics and process control

tel : +32 9 264 59 87
Joris.Meys at Ugent.be
-------------------------------
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