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

Fri Aug 8 11:17:47 CEST 2014

Hi,
In cases where the clusters are not so clear cut, it may be much more difficult, and anyway, the original quest was slightly different, I guess. Here is another example:
DAPC performed on pops (first figure) or DAPC without pop info (find.clusters) (second figure). As each dot on the second figure belongs to a sampled pop, can we get them coloured (without changing the plot) with colour codes as in the first figure? Apparently not… But was not that the original question?

Cheers
Rita

On 8 Aug, 2014, at 02:05, Nicolas Dussex <nicolas.dussex at gmail.com> wrote:

> 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
> _______________________________________________
> adegenet-forum mailing list
> adegenet-forum at lists.r-forge.r-project.org<mailto:adegenet-forum at lists.r-forge.r-project.org>
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum
> 
> _______________________________________________
> 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
> 
> _______________________________________________
> 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
> 
> _______________________________________________
> 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
> _______________________________________________
> 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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20140808/51acb34c/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: PastedGraphic-2.tiff
Type: image/tiff
Size: 295206 bytes
Desc: not available
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20140808/51acb34c/attachment-0002.tiff>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: PastedGraphic-3.tiff
Type: image/tiff
Size: 295206 bytes
Desc: not available
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20140808/51acb34c/attachment-0003.tiff>