[adegenet-forum] Population clustering idea

[Vladimir Mikryukov]

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 (ext.290),  +7 922 61 36 8

On Fri, Apr 29, 2011 at 10:10 PM, Mac Campbell <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
>
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