<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">So, why the warning: "the analysis is no longer optimal in terms of group discrimination”, if it is the same analysis...<br><div apple-content-edited="true"><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><br></div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Cheers</div><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Rita</div>
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<br><div><div>On 7 Aug, 2014, at 12:08, Jombart, Thibaut <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><br>Hi<br><br>this is what I understood too. And my answer does exactly that - see the grp argument in ?scatter.dapc.<br><br>Cheers<br>Thibaut<br>________________________________________<br>From: Emrah Coraman [<a href="mailto:coramane@gmail.com">coramane@gmail.com</a>]<br>Sent: 07 August 2014 12:01<br>To: Jombart, Thibaut<br>Cc: Nicolas Dussex; <a href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br>Subject: Re: [adegenet-forum] DAPC scatter plot and individual colour by population<br><br>Hi,<br><br>I think Nic just wants to color the DAPC scatter plot not with the identified DAPC groups but with their respective population information.<br>So I guess he doesn't want to change the group discrimination method.<br><br>Did I get it right?<br><br>Best wishes,<br>Emrah<br><br><br>On 7 August 2014 13:53, Jombart, Thibaut <<a href="mailto:t.jombart@imperial.ac.uk">t.jombart@imperial.ac.uk</a><<a href="mailto:t.jombart@imperial.ac.uk">mailto:t.jombart@imperial.ac.uk</a>>> wrote:<br>Hi there,<br><br>simple, just replace grp$grp with the grouping of individuals you want to use for the plot.<br><br>This said, be aware that the analysis is no longer optimal in terms of group discrimination.<br><br>Best<br>Thibaut<br><br><br>==============================<br>Dr Thibaut Jombart<br>MRC Centre for Outbreak Analysis and Modelling<br>Department of Infectious Disease Epidemiology<br>Imperial College - School of Public Health<br>Norfolk Place, London W2 1PG, UK<br>Tel. : 0044 (0)20 7594 3658<br><a href="http://sites.google.com/site/thibautjombart/">http://sites.google.com/site/thibautjombart/</a><br>http://sites.google.com/site/therepiproject/<br>http://adegenet.r-forge.r-project.org/<br>Twitter: @thibautjombart<br>________________________________________<br>From: adegenet-forum-bounces@lists.r-forge.r-project.org<mailto:adegenet-forum-bounces@lists.r-forge.r-project.org> [adegenet-forum-bounces@lists.r-forge.r-project.org<mailto:adegenet-forum-bounces@lists.r-forge.r-project.org>] on behalf of Nicolas Dussex [nicolas.dussex@gmail.com<mailto:nicolas.dussex@gmail.com>]<br>Sent: 07 August 2014 02:15<br>To: adegenet-forum@lists.r-forge.r-project.org<mailto:adegenet-forum@lists.r-forge.r-project.org><br>Subject: [adegenet-forum] DAPC scatter plot and individual colour by population<br><br>Hi,<br><br>I built a DAPC scatter plot without using a priori grouping information (i.e. geographically distinct populations) using this simple command line: dapc1 <- dapc(data, grp$grp).<br><br>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.<br><br>I couldn't find this information on the manual and was hoping I could get some advice on that.<br><br>Thanks for your help!<br>Nic<br>--<br>Nic Dussex PhD<br>Department of Zoology<br>University of Otago<br>340 Great King Street<br>P.O.Box 56<br>Dunedin 9054<br>New Zealand<br><br>Mobile: 021 02790938<br>_______________________________________________<br>adegenet-forum mailing list<br>adegenet-forum@lists.r-forge.r-project.org<mailto:adegenet-forum@lists.r-forge.r-project.org><br>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum<br><br>_______________________________________________<br>adegenet-forum mailing list<br>adegenet-forum@lists.r-forge.r-project.org<br>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum<br></blockquote></div><br></body></html>