[adegenet-forum] DAPC scatter plot and individual colour by population

[Nicolas Dussex]

Hi everyone,

Thanks for your help. Emrah is sort of right. I also  tried this command:

dapc1 <- dapc(data, *grp$pop*)

but the clustering seems a bit different from the grp$grp option. So I
would like to keep the clusters identified with the group discrimination
method but color my points according to their population of origin as in
this example:

http://figshare.com/articles/_Genetic_structure_of_the_PWN_field_samples_from_the_USA_/653650

but didn't find the information to do that sort of scatter plot in the
manual.

Hope it makes sense.

Cheers
Nic


On 8 August 2014 04:10, Jombart, Thibaut <t.jombart at imperial.ac.uk> wrote:

>
> You run an analysis using group 'yyy'. The analysis provides an optimum
> discrimination for group 'yyy'.
>
> Then if you plot the results using group 'zzz', the analysis is no longer
> optimum for this group. The analysis hasn't changed, and is still only
> optimal for 'yyy'.
>
> Cheers
> Thibaut
>
> ________________________________________
> From: adegenet-forum-bounces at lists.r-forge.r-project.org [
> adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Rita
> Castilho [rita.castil at gmail.com]
> Sent: 07 August 2014 16:27
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: Re: [adegenet-forum] DAPC scatter plot and individual colour by
>      population
>
> So, why the warning: "the analysis is no longer optimal in terms of group
> discrimination”, if it is the same analysis...
>
> Cheers
> Rita
>
> On 7 Aug, 2014, at 12:08, Jombart, Thibaut <t.jombart at imperial.ac.uk
> <mailto:t.jombart at imperial.ac.uk>> wrote:
>
>
> Hi
>
> this is what I understood too. And my answer does exactly that - see the
> grp argument in ?scatter.dapc.
>
> Cheers
> Thibaut
> ________________________________________
> From: Emrah Coraman [coramane at gmail.com<mailto:coramane at gmail.com>]
> Sent: 07 August 2014 12:01
> To: Jombart, Thibaut
> Cc: Nicolas Dussex; adegenet-forum at lists.r-forge.r-project.org<mailto:
> adegenet-forum at lists.r-forge.r-project.org>
> Subject: Re: [adegenet-forum] DAPC scatter plot and individual colour by
> population
>
> Hi,
>
> I think Nic just wants to color the DAPC scatter plot  not with the
> identified DAPC groups but with their respective population information.
> So I guess he doesn't want to change the group discrimination method.
>
> Did I get it right?
>
> Best wishes,
> Emrah
>
>
> On 7 August 2014 13:53, Jombart, Thibaut <t.jombart at imperial.ac.uk<mailto:
> t.jombart at imperial.ac.uk><mailto:t.jombart at imperial.ac.uk>> wrote:
> Hi there,
>
> simple, just replace grp$grp with the grouping of individuals you want to
> use for the plot.
>
> This said, be aware that the analysis is no longer optimal in terms of
> group discrimination.
>
> Best
> Thibaut
>
>
> ==============================
> Dr Thibaut Jombart
> MRC Centre for Outbreak Analysis and Modelling
> Department of Infectious Disease Epidemiology
> Imperial College - School of Public Health
> Norfolk Place, London W2 1PG, UK
> Tel. : 0044 (0)20 7594 3658
> http://sites.google.com/site/thibautjombart/
> http://sites.google.com/site/therepiproject/
> http://adegenet.r-forge.r-project.org/
> Twitter: @thibautjombart
> ________________________________________
> From: adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:
> adegenet-forum-bounces at lists.r-forge.r-project.org> [
> adegenet-forum-bounces at lists.r-forge.r-project.org<mailto:
> adegenet-forum-bounces at lists.r-forge.r-project.org>] on behalf of Nicolas
> Dussex [nicolas.dussex at gmail.com<mailto:nicolas.dussex at gmail.com>]
> Sent: 07 August 2014 02:15
> To: adegenet-forum at lists.r-forge.r-project.org<mailto:
> adegenet-forum at lists.r-forge.r-project.org>
> Subject: [adegenet-forum] DAPC scatter plot and individual colour by
>  population
>
> Hi,
>
> I built a DAPC scatter plot without using a priori grouping information
> (i.e. geographically distinct populations) using this simple command line:
> dapc1 <- dapc(data, grp$grp).
>
> I obtained three distinct cluster but now I was wondering how I could
>  represent each individual with a colour corresponding to their sampling
> origin rather than to their inferred cluster.
>
> I couldn't find this information on the manual and was hoping I could get
> some advice on that.
>
> Thanks for your help!
> Nic
> --
> Nic Dussex PhD
> Department of Zoology
> University of Otago
> 340 Great King Street
> P.O.Box 56
> Dunedin 9054
> New Zealand
>
> Mobile: 021 02790938
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-- 
Nic Dussex PhD
Department of Zoology
University of Otago
340 Great King Street
P.O.Box 56
Dunedin 9054
New Zealand

Mobile: 021 02790938
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