[adegenet-forum] Population clustering idea

[Jombart, Thibaut]

Hello,

that's a good question. Actually I thought about implementing something along these lines for the dapc scatterplot. I agree with Russell's point that relationships between populations are not necessarily best presented by fully bifurcating trees. However, linking the populations which are the closest according to a given distance measure (e.g. Fst ) does make sense. I would go for a minimum spanning tree, which is a nice way of showing which are the closest neighbours in terms of genetic distances. It won't be too much of a pain to code either.

I will be working on the next adegenet release over the weeks to come, so will probably give it a go soon.

Cheers

Thibaut
________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of Mac Campbell [macampbell2 at alaska.edu]
Sent: 29 April 2011 22:48
To: Vladimir Mikryukov
Cc: adegenet forum
Subject: Re: [adegenet-forum] Population clustering idea

Vladimir,

Hey, that worked great.

Thanks,

Mac

On Fri, Apr 29, 2011 at 9:17 AM, Vladimir Mikryukov <vmikryukov at gmail.com<mailto:vmikryukov at gmail.com>> wrote:
Here is a draft solution with the built in example:

library(adegenet)
data(H3N2)
pop(H3N2) <- factor(H3N2$other$epid)
dapc1 <- dapc(H3N2, all.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5)

hc <- hclust(dist(dapc1$grp.coord))
dend <- as.dendrogram(hc)
plot(dend)


HTH,
Vladimir

--
Vladimir Mikryukov
PhD student
Institute of Plant & Animal Ecology UD RAS,
Lab. of Population and Community Ecotoxicology
[8 Marta 202, 620144, Ekaterinburg, Russia]
Tel.  +7 343 210 38 58<tel:%2B7%20343%20210%2038%2058> (ext.290),  +7 922 61 36 8

On Fri, Apr 29, 2011 at 10:10 PM, Mac Campbell <macampbell2 at alaska.edu<mailto:macampbell2 at alaska.edu>> wrote:
Hi ,

I was looking at another grad students clustering analysis, and he displayed it as a tree.  It was some sort of ecological data.    Anyways, I thought it might be useful to compare groups identified through DAPC that way.  Display them graphically using adegenet, but also provide some sort of tree as a hypothesis of relationships.  It would seem to me that this could already by done in R without the need to develop anything new.  Does anybody have an idea how to take output from dapc and make a tree?

Mac



--
Matthew A Campbell
Department of Biology and Wildlife
University of Alaska, Fairbanks

_______________________________________________
adegenet-forum mailing list
adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum





--
Matthew A Campbell
Department of Biology and Wildlife
University of Alaska, Fairbanks
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20110430/c67701a8/attachment.htm>