<html><head></head><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:13px"><div id="yui_3_16_0_ym19_1_1508092281929_78876">Dear All (Kamvar, Jombart and Roman),</div><div id="yui_3_16_0_ym19_1_1508092281929_78877">First, I would like to thank you all for spending a little of your time on my problem. Unfortunely, it was not possible to do what I want with commands that you showed me. I think that I will have to write very carefully my work to explain my groups and my dots (haployd individuals) inside of the groups formed by DAPC analysis. </div><div id="yui_3_16_0_ym19_1_1508092281929_78878">Obs: Kamvar, your command is very useful, but it was not possible to have dots with different colors or forms inside of the same group.</div><div id="yui_3_16_0_ym19_1_1508092281929_78879"><br id="yui_3_16_0_ym19_1_1508092281929_78880"></div><div id="yui_3_16_0_ym19_1_1508092281929_78881"><br id="yui_3_16_0_ym19_1_1508092281929_78882"></div><div id="yui_3_16_0_ym19_1_1508092281929_78883">Best regards,</div><div id="yui_3_16_0_ym19_1_1508092281929_78864"></div><div dir="ltr" id="yui_3_16_0_ym19_1_1508092281929_78884">Lucas Veiga Ayres Pimenta</div> <div class="qtdSeparateBR"><br><br></div><div class="yahoo_quoted" style="display: block;"> <div style="font-family: times new roman, new york, times, serif; font-size: 13px;"> <div style="font-family: HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif; font-size: 16px;"> <div dir="ltr"><font size="2" face="Arial"> Em Sexta-feira, 13 de Outubro de 2017 12:48, Zhian Kamvar <zkamvar@gmail.com> escreveu:<br></font></div> <br><br> <div class="y_msg_container"><div id="yiv3214801232"><div>Hi,<div class="yiv3214801232"><br class="yiv3214801232"></div><div class="yiv3214801232">The individual coordinates are in the @ind.coord slot of the DAPC object. You can use those to plot and color them with your desired population factor.</div><div class="yiv3214801232"><br class="yiv3214801232"></div><div class="yiv3214801232">I have recently come up with a ggplot2 solution for this: <a rel="nofollow" target="_blank" href="https://github.com/everhartlab/sclerotinia-366/blame/v1.0/results/by-year.md#L508-L558" class="yiv3214801232">https://github.com/everhartlab/sclerotinia-366/blame/v1.0/results/by-year.md#L508-L558</a>, the results of which look like so: <a rel="nofollow" target="_blank" href="https://github.com/everhartlab/sclerotinia-366/blob/v1.0/results/figures/by-year/dapc_plot-2.png" class="yiv3214801232">https://github.com/everhartlab/sclerotinia-366/blob/v1.0/results/figures/by-year/dapc_plot-2.png</a></div><div class="yiv3214801232"><br class="yiv3214801232"></div><div class="yiv3214801232">Hope that helps,</div><div class="yiv3214801232">Zhian</div><div class="yiv3214801232"><br class="yiv3214801232"><div class="yiv3214801232">
<div style="word-wrap:break-word;" class="yiv3214801232"><div style="color:rgb(0, 0, 0);font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;">-----</div><div style="color:rgb(0, 0, 0);font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;">Zhian N. Kamvar, Ph. D.</div><div style="color:rgb(0, 0, 0);font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;">Postdoctoral Researcher (Everhart Lab)</div><div style="color:rgb(0, 0, 0);font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;">Department of Plant Pathology</div><div style="color:rgb(0, 0, 0);font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;">University of Nebraska-Lincoln</div><div style="color:rgb(0, 0, 0);font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;">ORCID: 0000-0003-1458-7108</div><div style="color:rgb(0, 0, 0);font-family:Helvetica;font-size:12px;font-style:normal;font-weight:normal;letter-spacing:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;" class="yiv3214801232"><br class="yiv3214801232"></div><br class="yiv3214801232Apple-interchange-newline"></div><br class="yiv3214801232Apple-interchange-newline">
</div>
<br class="yiv3214801232"><div><blockquote type="cite" class="yiv3214801232"><div class="yiv3214801232">On Oct 13, 2017, at 03:39 , <a rel="nofollow" ymailto="mailto:adegenet-forum-request@lists.r-forge.r-project.org" target="_blank" href="mailto:adegenet-forum-request@lists.r-forge.r-project.org" class="yiv3214801232">adegenet-forum-request@lists.r-forge.r-project.org</a> wrote:</div><br class="yiv3214801232Apple-interchange-newline"><div class="yiv3214801232"><div class="yiv3214801232">Send adegenet-forum mailing list submissions to<br class="yiv3214801232"><span class="yiv3214801232Apple-tab-span" style="white-space:pre;"> </span><a rel="nofollow" ymailto="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank" href="mailto:adegenet-forum@lists.r-forge.r-project.org" class="yiv3214801232">adegenet-forum@lists.r-forge.r-project.org</a><br class="yiv3214801232"><br class="yiv3214801232">To subscribe or unsubscribe via the World Wide Web, visit<br class="yiv3214801232"><span class="yiv3214801232Apple-tab-span" style="white-space:pre;"> </span>https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum<br class="yiv3214801232"><br class="yiv3214801232">or, via email, send a message with subject or body 'help' to<br class="yiv3214801232"><span class="yiv3214801232Apple-tab-span" style="white-space:pre;"> </span>adegenet-forum-request@lists.r-forge.r-project.org<br class="yiv3214801232"><br class="yiv3214801232">You can reach the person managing the list at<br class="yiv3214801232"><span class="yiv3214801232Apple-tab-span" style="white-space:pre;"> </span>adegenet-forum-owner@lists.r-forge.r-project.org<br class="yiv3214801232"><br class="yiv3214801232">When replying, please edit your Subject line so it is more specific<br class="yiv3214801232">than "Re: Contents of adegenet-forum digest..."<br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232">Today's Topics:<br class="yiv3214801232"><br class="yiv3214801232"> 1. Re: Dots in the DAPC graphic (Lucas Veiga)<br class="yiv3214801232"> 2. Re: Dots in the DAPC graphic (Lucas Veiga)<br class="yiv3214801232"> 3. Re: Dots in the DAPC graphic (Roman Lu?trik)<br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232">----------------------------------------------------------------------<br class="yiv3214801232"><br class="yiv3214801232">Message: 1<br class="yiv3214801232">Date: Thu, 12 Oct 2017 12:03:35 +0000 (UTC)<br class="yiv3214801232">From: Lucas Veiga <lucasfip@yahoo.com.br><br class="yiv3214801232">To: Roman Lu?trik <roman.lustrik@biolitika.si><br class="yiv3214801232">Cc: "adegenet-forum@lists.r-forge.r-project.org"<br class="yiv3214801232"><span class="yiv3214801232Apple-tab-span" style="white-space:pre;"> </span><adegenet-forum@lists.r-forge.r-project.org><br class="yiv3214801232">Subject: Re: [adegenet-forum] Dots in the DAPC graphic<br class="yiv3214801232">Message-ID: <1994389766.433362.1507809815326@mail.yahoo.com><br class="yiv3214801232">Content-Type: text/plain; charset="utf-8"<br class="yiv3214801232"><br class="yiv3214801232">Dear Roman,First, thank you for the help. Unfortunaly, apparently your command not worked for me. I will try explain better my situation. I work with phytopathology and the fungus that I work affects different crops (I have put in my input file .csv the crops as my populations, different crops are different populations). Due the migration of genotypes of the fungus between the crops, inside of one group formed by DAPC there are genotypes obtained of different crops (populations) and for better viewing of this migration I want to plot the dots according of the hosts and not according of the groups formed by DAPC analysis. So, inside of one group there will are dots of different colors.?I hope have explain better my situation and that you can help me.<br class="yiv3214801232">Best regards,Lucas Veiga Ayres pimenta <br class="yiv3214801232"><br class="yiv3214801232"> Em Quinta-feira, 12 de Outubro de 2017 5:49, Roman Lu?trik <roman.lustrik@biolitika.si> escreveu:<br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232"> Map `grp` argument to your desired grouping. Make sure that you pass `col` the correct number of colors which should match the number of groups you are specifying.<br class="yiv3214801232">By default, coloring is done on grouping (see here). See this example:<br class="yiv3214801232">library(adegenet)<br class="yiv3214801232"><br class="yiv3214801232">data(H3N2)<br class="yiv3214801232">pop(H3N2) <- factor(H3N2$other$epid)<br class="yiv3214801232">dapc1 <- dapc(H3N2, var.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5)<br class="yiv3214801232"><br class="yiv3214801232">data.frame(dapc1$grp, pop(H3N2)) # they are matching<br class="yiv3214801232"><br class="yiv3214801232">Cheers,Roman<br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232">----<br class="yiv3214801232">In god we trust, all others bring data.<br class="yiv3214801232"><blockquote type="cite" class="yiv3214801232">Zahtevaj IJZ na https://kurc.biolitika.si<br class="yiv3214801232"></blockquote>From: "Lucas Veiga" <lucasfip@yahoo.com.br><br class="yiv3214801232">To: adegenet-forum@lists.r-forge.r-project.org<br class="yiv3214801232">Sent: Thursday, October 12, 2017 1:34:19 AM<br class="yiv3214801232">Subject: [adegenet-forum] Dots in the DAPC graphic<br class="yiv3214801232"><br class="yiv3214801232">Dear all,I would like to know what I can do for the dots in DAPC graph to be colored according to the populations and not according to the DAPC analysis groups?<br class="yiv3214801232"><br class="yiv3214801232">Best regards,<br class="yiv3214801232">Lucas Veiga Ayres Pimenta<br class="yiv3214801232">_______________________________________________<br class="yiv3214801232">adegenet-forum mailing list<br class="yiv3214801232">adegenet-forum@lists.r-forge.r-project.org<br class="yiv3214801232">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum<br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232">-------------- next part --------------<br class="yiv3214801232">An HTML attachment was scrubbed...<br class="yiv3214801232">URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20171012/c5b29746/attachment-0001.html><br class="yiv3214801232"><br class="yiv3214801232">------------------------------<br class="yiv3214801232"><br class="yiv3214801232">Message: 2<br class="yiv3214801232">Date: Thu, 12 Oct 2017 12:10:28 +0000 (UTC)<br class="yiv3214801232">From: Lucas Veiga <lucasfip@yahoo.com.br><br class="yiv3214801232">To: Roman Lu?trik <roman.lustrik@biolitika.si><br class="yiv3214801232">Cc: "adegenet-forum@lists.r-forge.r-project.org"<br class="yiv3214801232"><span class="yiv3214801232Apple-tab-span" style="white-space:pre;"> </span><adegenet-forum@lists.r-forge.r-project.org><br class="yiv3214801232">Subject: Re: [adegenet-forum] Dots in the DAPC graphic<br class="yiv3214801232">Message-ID: <342879047.415645.1507810228644@mail.yahoo.com><br class="yiv3214801232">Content-Type: text/plain; charset="utf-8"<br class="yiv3214801232"><br class="yiv3214801232">Dear Roman,First, thank you for the help. Unfortunaly, apparently your command not worked for me. I will try explain better my situation. I work with phytopathology and the fungus that I work affects different crops (I have put in my input file .csv the crops as my populations, different crops are different populations). Due the migration of genotypes of the fungus between the crops, inside of one group formed by DAPC there are genotypes obtained of different crops (populations) and for better viewing of this migration I want to plot the dots according to the hosts and not according to the groups formed by DAPC analysis. So, inside of one group there will are dots of different colors.?I hope I have explained better my situation and that you can help me.<br class="yiv3214801232">Best regards,Lucas Veiga Ayres pimenta <br class="yiv3214801232"><br class="yiv3214801232"> Em Quinta-feira, 12 de Outubro de 2017 9:03, Lucas Veiga <lucasfip@yahoo.com.br> escreveu:<br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232"> Dear Roman,First, thank you for the help. Unfortunaly, apparently your command not worked for me. I will try explain better my situation. I work with phytopathology and the fungus that I work affects different crops (I have put in my input file .csv the crops as my populations, different crops are different populations). Due the migration of genotypes of the fungus between the crops, inside of one group formed by DAPC there are genotypes obtained of different crops (populations) and for better viewing of this migration I want to plot the dots according of the hosts and not according of the groups formed by DAPC analysis. So, inside of one group there will are dots of different colors.?I hope have explain better my situation and that you can help me.<br class="yiv3214801232">Best regards,Lucas Veiga Ayres pimenta <br class="yiv3214801232"><br class="yiv3214801232"> Em Quinta-feira, 12 de Outubro de 2017 5:49, Roman Lu?trik <roman.lustrik@biolitika.si> escreveu:<br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232"> Map `grp` argument to your desired grouping. Make sure that you pass `col` the correct number of colors which should match the number of groups you are specifying.<br class="yiv3214801232">By default, coloring is done on grouping (see here). See this example:<br class="yiv3214801232">library(adegenet)<br class="yiv3214801232"><br class="yiv3214801232">data(H3N2)<br class="yiv3214801232">pop(H3N2) <- factor(H3N2$other$epid)<br class="yiv3214801232">dapc1 <- dapc(H3N2, var.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5)<br class="yiv3214801232"><br class="yiv3214801232">data.frame(dapc1$grp, pop(H3N2)) # they are matching<br class="yiv3214801232"><br class="yiv3214801232">Cheers,Roman<br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232">----<br class="yiv3214801232">In god we trust, all others bring data.<br class="yiv3214801232"><blockquote type="cite" class="yiv3214801232">Zahtevaj IJZ na https://kurc.biolitika.si<br class="yiv3214801232"></blockquote>From: "Lucas Veiga" <lucasfip@yahoo.com.br><br class="yiv3214801232">To: adegenet-forum@lists.r-forge.r-project.org<br class="yiv3214801232">Sent: Thursday, October 12, 2017 1:34:19 AM<br class="yiv3214801232">Subject: [adegenet-forum] Dots in the DAPC graphic<br class="yiv3214801232"><br class="yiv3214801232">Dear all,I would like to know what I can do for the dots in DAPC graph to be colored according to the populations and not according to the DAPC analysis groups?<br class="yiv3214801232"><br class="yiv3214801232">Best regards,<br class="yiv3214801232">Lucas Veiga Ayres Pimenta<br class="yiv3214801232">_______________________________________________<br class="yiv3214801232">adegenet-forum mailing list<br class="yiv3214801232">adegenet-forum@lists.r-forge.r-project.org<br class="yiv3214801232">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum<br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232">-------------- next part --------------<br class="yiv3214801232">An HTML attachment was scrubbed...<br class="yiv3214801232">URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20171012/32d4d4d6/attachment-0001.html><br class="yiv3214801232"><br class="yiv3214801232">------------------------------<br class="yiv3214801232"><br class="yiv3214801232">Message: 3<br class="yiv3214801232">Date: Fri, 13 Oct 2017 10:38:57 +0200 (CEST)<br class="yiv3214801232">From: Roman Lu?trik <roman.lustrik@biolitika.si><br class="yiv3214801232">To: Lucas Veiga <lucasfip@yahoo.com.br><br class="yiv3214801232">Cc: adegenet-forum@lists.r-forge.r-project.org<br class="yiv3214801232">Subject: Re: [adegenet-forum] Dots in the DAPC graphic<br class="yiv3214801232">Message-ID:<br class="yiv3214801232"><span class="yiv3214801232Apple-tab-span" style="white-space:pre;"> </span><181441774.286421.1507883937636.JavaMail.zimbra@biolitika.si><br class="yiv3214801232">Content-Type: text/plain; charset="utf-8"<br class="yiv3214801232"><br class="yiv3214801232">A-ha, I think I see where you're getting at. Right now I'm not sure it's possible to have DAPC groups with samples colored by some specific variable. Perhaps Thibaut will be able to chime in. If I'm right, this is something we could think about in the upcoming releases. <br class="yiv3214801232"><br class="yiv3214801232">In the mean time, you can construct your own plot, taking bits and pieces from https://github.com/thibautjombart/adegenet/blob/master/R/dapc.R#L539 <br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232">Cheers, <br class="yiv3214801232">Roman <br class="yiv3214801232"><br class="yiv3214801232">---- <br class="yiv3214801232">In god we trust, all others bring data. <br class="yiv3214801232"><blockquote type="cite" class="yiv3214801232">Zahtevaj IJZ na https://kurc.biolitika.si <br class="yiv3214801232"></blockquote><br class="yiv3214801232"><br class="yiv3214801232">From: "Lucas Veiga" <lucasfip@yahoo.com.br> <br class="yiv3214801232">To: "Roman Lu?trik" <roman.lustrik@biolitika.si> <br class="yiv3214801232">Cc: adegenet-forum@lists.r-forge.r-project.org <br class="yiv3214801232">Sent: Thursday, October 12, 2017 2:03:35 PM <br class="yiv3214801232">Subject: Re: [adegenet-forum] Dots in the DAPC graphic <br class="yiv3214801232"><br class="yiv3214801232">Dear Roman, <br class="yiv3214801232">First, thank you for the help. Unfortunaly, apparently your command not worked for me. I will try explain better my situation. I work with phytopathology and the fungus that I work affects different crops (I have put in my input file .csv the crops as my populations, different crops are different populations). Due the migration of genotypes of the fungus between the crops, inside of one group formed by DAPC there are genotypes obtained of different crops (populations) and for better viewing of this migration I want to plot the dots according of the hosts and not according of the groups formed by DAPC analysis. So, inside of one group there will are dots of different colors. <br class="yiv3214801232">I hope have explain better my situation and that you can help me. <br class="yiv3214801232"><br class="yiv3214801232">Best regards, <br class="yiv3214801232">Lucas Veiga Ayres pimenta <br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232">Em Quinta-feira, 12 de Outubro de 2017 5:49, Roman Lu?trik <roman.lustrik@biolitika.si> escreveu: <br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232">Map `grp` argument to your desired grouping. Make sure that you pass `col` the correct number of colors which should match the number of groups you are specifying. <br class="yiv3214801232">By default, coloring is done on grouping ( see here ). See this example: <br class="yiv3214801232"><br class="yiv3214801232">library(adegenet) <br class="yiv3214801232"><br class="yiv3214801232">data(H3N2) <br class="yiv3214801232">pop(H3N2) <- factor(H3N2$other$epid) <br class="yiv3214801232">dapc1 <- dapc(H3N2, var.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5) <br class="yiv3214801232"><br class="yiv3214801232">data.frame(dapc1$grp, pop(H3N2)) # they are matching <br class="yiv3214801232"><br class="yiv3214801232">Cheers, <br class="yiv3214801232">Roman <br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232">---- <br class="yiv3214801232">In god we trust, all others bring data. <br class="yiv3214801232"><blockquote type="cite" class="yiv3214801232">Zahtevaj IJZ na https://kurc.biolitika.si <br class="yiv3214801232"></blockquote><br class="yiv3214801232"><br class="yiv3214801232">From: "Lucas Veiga" <lucasfip@yahoo.com.br> <br class="yiv3214801232">To: adegenet-forum@lists.r-forge.r-project.org <br class="yiv3214801232">Sent: Thursday, October 12, 2017 1:34:19 AM <br class="yiv3214801232">Subject: [adegenet-forum] Dots in the DAPC graphic <br class="yiv3214801232"><br class="yiv3214801232">Dear all, <br class="yiv3214801232">I would like to know what I can do for the dots in DAPC graph to be colored according to the populations and not according to the DAPC analysis groups? <br class="yiv3214801232"><br class="yiv3214801232">Best regards, <br class="yiv3214801232">Lucas Veiga Ayres Pimenta <br class="yiv3214801232"><br class="yiv3214801232">_______________________________________________ <br class="yiv3214801232">adegenet-forum mailing list <br class="yiv3214801232">adegenet-forum@lists.r-forge.r-project.org <br class="yiv3214801232">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum <br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232"><br class="yiv3214801232">-------------- next part --------------<br class="yiv3214801232">An HTML attachment was scrubbed...<br class="yiv3214801232">URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20171013/aedaf8eb/attachment.html><br class="yiv3214801232"><br class="yiv3214801232">------------------------------<br class="yiv3214801232"><br class="yiv3214801232">_______________________________________________<br class="yiv3214801232">adegenet-forum mailing list<br class="yiv3214801232">adegenet-forum@lists.r-forge.r-project.org<br class="yiv3214801232">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum<br class="yiv3214801232"><br class="yiv3214801232">End of adegenet-forum Digest, Vol 110, Issue 11<br class="yiv3214801232">***********************************************<br class="yiv3214801232"></div></div></blockquote></div><br class="yiv3214801232"></div></div></div>_______________________________________________<br>adegenet-forum mailing list<br><a ymailto="mailto:adegenet-forum@lists.r-forge.r-project.org" href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge.r-project.org</a><br><a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum" target="_blank">https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum</a><br><br></div> </div> </div> </div></div></body></html>