[adegenet-forum] Population clustering idea

[Mac Campbell]

Hi,

Yes, I agree there are many limitations to viewing populations in a tree
like perspective.  Initially, I was interested in quantifying how far apart
the groups are on a scatter plot because it was hard to tell.  I think the
code Vladimir sent me does just that, at least it tells me which ones are
closer to each other.

It will be cool to have a more biologically significant (Fst based)  way
implemented.  One thing that came to mind too was if I wanted to use
something like IMa2, I would need to have an assumption in tree form of how
the populations are related.

Mac

On Sat, Apr 30, 2011 at 8:56 AM, Jombart, Thibaut
<t.jombart at imperial.ac.uk>wrote:

>  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>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
>>>
>>>  _______________________________________________
>>> adegenet-forum mailing list
>>> 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
>



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