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

[Nicolas Dussex]

I think I understand now. So I guess that in the following figure (
http://figshare.com/articles/_Genetic_structure_of_the_PWN_field_samples_from_the_USA_/653650),
they ran the analysis using *grp$pop *without the  population ellipses and
simply draw the clusters manually. At least that is how I understand it.

Thanks for your help!
Nic


On 8 August 2014 09:38, Emrah Coraman <coramane at gmail.com> wrote:

> 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
>>
>> _______________________________________________
>> 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
>>
>
>


-- 
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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