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

[Emrah Coraman]

Hi Nic,

That's what I thought as well.
But indeed you have to change the argument when using the scatter.dapc
argument as Thimbaut pointed.

Best wishes,
Emrah



On 8 August 2014 00:27, Nicolas Dussex <nicolas.dussex at gmail.com> wrote:

> 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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