[adegenet-forum] Population clustering idea

[Mac Campbell]

Vladimir,

Hey, that worked great.

Thanks,

Mac

On Fri, Apr 29, 2011 at 9:17 AM, Vladimir Mikryukov <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 (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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>>
>>
>


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