[adegenet-forum] How to interpret Density Plot for K=2

[Thibaut Jombart]

Hi there,

I would definitely second Mark's comment and use cross-validation here.

Also for the clustering, I would give snapclust a try - I have just pushed
a new version on github which is now properly documented. Especially check
what the 'optimal k' is according to the various goodness of fit stats
(snapclust.choose.k) - AIC, AICc, BIC, KIC.

Best
Thibaut


--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
WHO Consultant - outbreak analysis
https://thibautjombart.netlify.com
Twitter: @TeebzR
+44(0)20 7594 3658

On 1 February 2018 at 20:36, Mark Coulson <Mark.Coulson.ic at uhi.ac.uk> wrote:

> Hi Nikki,
>
>
>
> Your interpretation of the plot seems correct, however I’d ask if you ran
> the xvalDAPC cross validation? It may be that you have kept too many PCs so
> are overfitting the data. The xvalDAPC will find the optimal number of PCs
> to retain for your two groups. Then use this number of PCs to run a new
> DAPC. It will likely result in more overlap between the two groups, which
> would then be more consistent with the low differentiation you are seeing
> based on FST.
>
>
>
> Hope this helps.
>
>
>
> Mark
>
>
>
> *From:* adegenet-forum-bounces at lists.r-forge.r-project.org [mailto:
> adegenet-forum-bounces at lists.r-forge.r-project.org] *On Behalf Of *Nikki
> Vollmer
> *Sent:* 30 January 2018 18:08
> *To:* adegenet-forum at lists.r-forge.r-project.org
> *Subject:* [adegenet-forum] How to interpret Density Plot for K=2
>
>
>
> Hi,
>
>
>
> I am trying to analyze ~200 RADseq loci for ~200 individuals.  STRUCTURE
> results suggest the best number of populations given the data is 2.
> Pairwise Fst values are quite low for my taxa (<0.003) with pvalue
> 0.01802.  I was trying to do a DAPC on this same data to compare results.
> DAPC similarly suggested the best # of clusters is 2 and I was able to plot
> a 1-dimensional density plot for the one DF I kept (attached).  However, I
> am not sure how to interpret the plot.  Is it correct to say that because
> the two peaks do not overlap that suggests the 2 clusters are quite
> differentiated from one another (similar to two clusters on a scatter plot
> being in opposite quadrants)?  (...or is that logic flawed?)
>
>
>
> I am trying to figure out if these 2 groups are very genetically
> differentiated or not, and I am not clear what the density plot is
> supporting/suggesting.
>
>
>
> I very much appreciate any guidance on this matter!
>
>
>
> Thank you,
>
> Nikki
>
>
> Inverness College UHI, a partner in the University of the Highlands and
> Islands www.inverness.uhi.ac.uk Board of Management of Inverness College
> (known as Inverness College UHI), Scottish Charity No SC021197.
>
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