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

[Emrah Coraman]

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> wrote:

> Hi there,
>
> simple, just replace grp$grp with the grouping of individuals you want to
> use for the plot.
>
> This said, be aware that the analysis is no longer optimal in terms of
> group discrimination.
>
> Best
> Thibaut
>
>
> ==============================
> Dr Thibaut Jombart
> MRC Centre for Outbreak Analysis and Modelling
> Department of Infectious Disease Epidemiology
> Imperial College - School of Public Health
> Norfolk Place, London W2 1PG, UK
> Tel. : 0044 (0)20 7594 3658
> http://sites.google.com/site/thibautjombart/
> http://sites.google.com/site/therepiproject/
> http://adegenet.r-forge.r-project.org/
> Twitter: @thibautjombart
> ________________________________________
> From: adegenet-forum-bounces at lists.r-forge.r-project.org [
> adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Nicolas
> Dussex [nicolas.dussex at gmail.com]
> Sent: 07 August 2014 02:15
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] DAPC scatter plot and individual colour by
>  population
>
> Hi,
>
> I built a DAPC scatter plot without using a priori grouping information
> (i.e. geographically distinct populations) using this simple command line:
> dapc1 <- dapc(data, grp$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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