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<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Arial",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Arial",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Arial",sans-serif;color:#1F497D;mso-fareast-language:EN-US">That’s great news Lucas.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Arial",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Arial",sans-serif;color:#1F497D;mso-fareast-language:EN-US">I wonder whether you would mind posting a version of your solution so others can make use of it in the future?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Arial",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Arial",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Cheers,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Arial",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Olly<o:p></o:p></span></p>
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<b><span style="font-size:10.0pt;line-height:115%;font-family:"Century Gothic",sans-serif;color:teal">Oliver Berry<o:p></o:p></span></b></p>
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<span style="font-size:10.0pt;line-height:115%;font-family:"Century Gothic",sans-serif;color:#31849B">Leader, Environomics Future Science Platform<o:p></o:p></span></p>
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<span style="font-size:10.0pt;line-height:115%;font-family:"Century Gothic",sans-serif;color:#31849B">CSIRO National Collections and Marine Infrastructure<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Century Gothic",sans-serif;color:#31849B">Indian Ocean Marine Research Centre<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Century Gothic",sans-serif;color:#31849B">The University of Western Australia, M097, 35 Stirling Highway<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Century Gothic",sans-serif;color:#31849B">Crawley, W.A., 6009, Australia
<o:p></o:p></span></p>
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<b><span style="font-size:10.0pt;line-height:115%;font-family:"Century Gothic",sans-serif;color:#31849B">P</span></b><span style="font-size:10.0pt;line-height:115%;font-family:"Century Gothic",sans-serif;color:#31849B">: +61-8-9333-6584
<b>F: </b>+61-8-9333-6555</span><span style="font-size:10.0pt;line-height:115%;font-family:"Century Gothic",sans-serif;color:#1F497D">
</span><b><span style="font-size:10.0pt;line-height:115%;font-family:"Century Gothic",sans-serif;color:teal">E</span></b><span style="font-size:10.0pt;line-height:115%;font-family:"Century Gothic",sans-serif;color:teal">:
<a href="mailto:Oliver.Berry@csiro.au">Oliver.Berry@csiro.au</a> <b>W</b>: </span>
<span style="font-size:10.0pt;line-height:115%;font-family:"Century Gothic",sans-serif;color:#1F497D"><a href="https://research.csiro.au/environomics/">Environomics</a></span><u><span style="font-size:10.0pt;line-height:115%;font-family:"Calibri",sans-serif;color:blue"><o:p></o:p></span></u></p>
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<p class="MsoNormal"><span lang="EN-AU" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Arial",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:14.0pt;font-family:"Arial",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Lucas Veiga [mailto:lucasfip@yahoo.com.br]
<br>
<b>Sent:</b> Thursday, 19 October 2017 7:55 AM<br>
<b>To:</b> adegenet-forum@lists.r-forge.r-project.org; Berry, Olly (NCMI, IOMRC Crawley) <Oliver.Berry@csiro.au><br>
<b>Subject:</b> Re: [adegenet-forum] Dots in the DAPC graphic (Lucas Veiga)<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt;background:white"><span style="font-size:10.0pt;color:black">Dear all,<br id="yui_3_16_0_ym19_1_1508369539247_14597">
Good news!! I did it making a little change in the s.class command. Oliver, your tip helped me a lot. Thanks all.<br id="yui_3_16_0_ym19_1_1508369539247_14598">
<br id="yui_3_16_0_ym19_1_1508369539247_14599">
Best regards,<br id="yui_3_16_0_ym19_1_1508369539247_14600">
Lucas Veiga Ayres Pimenta<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><a href="http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail" target="_blank"><span style="text-decoration:none"><img border="0" width="46" height="29" id="_x0000_i1025" src="https://ipmcdn.avast.com/images/icons/icon-envelope-tick-green-avg-v1.png"></span></a><o:p></o:p></p>
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<p class="MsoNormal" style="line-height:13.5pt"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#41424E">Livre de vírus.
<a href="http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail" target="_blank" id="yui_3_16_0_ym19_1_1508369539247_14682">
<span style="color:#4453EA">www.avg.com</span></a>. <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:black">Em Terça-feira, 17 de Outubro de 2017 8:23, Shannon O'Leary <<a href="mailto:shannon.j.oleary@gmail.com">shannon.j.oleary@gmail.com</a>>
escreveu:</span><span style="font-family:"Helvetica",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt;background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">Hi Lucas,<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">Try this on for size: <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">From your description it looks like you have a data set for which you have the following information:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">SAMPLE-ID | POPULATION (CROP) | GENOTYPES<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">you read in the genotypes as a genind object (gen) and your can read in your sample information as a dataframe containing Sample_ID and POP information
(SampleInfo)<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">You then ran k-means clustering/DAPC on your data set, something like this<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">grp <- find.clusters.genind(gen, n.pca = 200,<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"> stat = "BIC", choose.n.clust = FALSE, criterion = "min",<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"> max.n.clust = 40)<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">dapc <-dapc(gen, grp$grp, n.pca = 50, n.da = 2)<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">You can pull the information on which sample was assigned to which cluster like so:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">clusters <- as.data.frame(grp$grp) %>%<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"> rownames_to_column("SAMPLE_ID") %>%<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"> rename(CLUSTER = `grp$grp`)<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">You can add this information to your SampleInfo dataframe using dplyr::left_join()<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">SampleInfo <- left_join(SampleInfo, clusters, by = "SAMPLE_ID")<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">resulting in a dataframe with 3 columns: SAMPLE_ID | CROP | CLUSTER.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">Now you can pull the coordinates from the dapc and also add them to that data frame as well:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">DAPC_Ind <- as.data.frame(dapc$ind.coord) %>%<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"> rownames_to_column("SAMPLE_ID")<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">SampleInfo <- left_join(SampleInfo, DAPC_Ind, by = "SAMPLE_ID")<o:p></o:p></span></p>
</div>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">Now you have a data frame that should look something like this<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">SAMPLE_ID | CROP | CLUSTER | LD1 | LD2 ...<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">Now you can plot your data using ggplot and you can adjust the shape and color of your data points as you please, for example:<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">ggplot(SampleInfo, aes(x = LD1, y = LD2), color = CROP, shape = CLUSTER) +<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">geom_point()<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">Is this what you are trying to achieve? You'll have to tweak the "code" I've thrown in here to fit your data (column names etc).<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">Shannon<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><br clear="all">
<o:p></o:p></span></p>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#545454">><(((jº> ><(((jº> ><(((jº> ><(((jº> </span><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#545454">><(((jº> ><(((jº>
><(((jº> </span><span style="font-family:"Helvetica",sans-serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-size:9.5pt;font-family:"Helvetica",sans-serif;color:black">Shannon J. O'Leary</span><span style="font-family:"Helvetica",sans-serif;color:black"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">Postdoctoral Research Associate<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">Marine Genomics Lab<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">Life Science Department<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">Texas A&M Corpus Christi<o:p></o:p></span></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">On Mon, Oct 16, 2017 at 12:11 PM, <<a href="mailto:adegenet-forum-request@lists.r-forge.r-project.org" target="_blank">adegenet-forum-request@lists.r-forge.r-project.org</a>>
wrote:<o:p></o:p></span></p>
<blockquote style="border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-right:0cm">
<p class="MsoNormal" style="background:white"><span style="font-family:"Helvetica",sans-serif;color:black">Send adegenet-forum mailing list submissions to<br>
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or, via email, send a message with subject or body 'help' to<br>
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Today's Topics:<br>
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1. Re: Dots in the DAPC graphic (Lucas Veiga)<br>
<br>
<br>
------------------------------ ------------------------------ ----------<br>
<br>
Message: 1<br>
Date: Mon, 16 Oct 2017 17:10:49 +0000 (UTC)<br>
From: Lucas Veiga <<a href="mailto:lucasfip@yahoo.com.br" target="_blank">lucasfip@yahoo.com.br</a>><br>
To: Zhian Kamvar <<a href="mailto:zkamvar@gmail.com" target="_blank">zkamvar@gmail.com</a>>,<br>
"<a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge. r-project.org</a>"<br>
<<a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge. r-project.org</a>><br>
Subject: Re: [adegenet-forum] Dots in the DAPC graphic<br>
Message-ID: <<a href="mailto:1729769391.894921.1508173849615@mail.yahoo.com" target="_blank">1729769391.894921. 1508173849615@mail.yahoo.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear All (Kamvar, Jombart and Roman),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.?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.<br>
<br>
Best regards,Lucas Veiga Ayres Pimenta<br>
<br>
Em Sexta-feira, 13 de Outubro de 2017 12:48, Zhian Kamvar <<a href="mailto:zkamvar@gmail.com" target="_blank">zkamvar@gmail.com</a>> escreveu:<br>
<br>
<br>
Hi,<br>
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.<br>
I have recently come up with a ggplot2 solution for this:?<a href="https://github.com/everhartlab/sclerotinia-366/blame/v1.0/results/by-year.md#L508-L558" target="_blank">https://github.com/ everhartlab/sclerotinia-366/ blame/v1.0/results/by-year.md# L508-L558</a>,
the results of which look like so:?<a href="https://github.com/everhartlab/sclerotinia-366/blob/v1.0/results/figures/by-year/dapc_plot-2.png" target="_blank">https://github.com/ everhartlab/sclerotinia-366/ blob/v1.0/results/figures/by- year/dapc_plot-2.png</a><br>
Hope that helps,Zhian<br>
-----Zhian N. Kamvar, Ph. D.Postdoctoral Researcher (Everhart Lab)Department of Plant PathologyUniversity of Nebraska-LincolnORCID:?0000- 0003-1458-7108<br>
<br>
<br>
<br>
<br>
On Oct 13, 2017, at 03:39 , <a href="mailto:adegenet-forum-request@lists.r-forge.r-project.org" target="_blank">
adegenet-forum-request@lists. r-forge.r-project.org</a> wrote:<br>
Send adegenet-forum mailing list submissions to<br>
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or, via email, send a message with subject or body 'help' to<br>
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When replying, please edit your Subject line so it is more specific<br>
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Today's Topics:<br>
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??1. Re: Dots in the DAPC graphic (Lucas Veiga)<br>
??2. Re: Dots in the DAPC graphic (Lucas Veiga)<br>
??3. Re: Dots in the DAPC graphic (Roman Lu?trik)<br>
<br>
<br>
------------------------------ ------------------------------ ----------<br>
<br>
Message: 1<br>
Date: Thu, 12 Oct 2017 12:03:35 +0000 (UTC)<br>
From: Lucas Veiga <<a href="mailto:lucasfip@yahoo.com.br" target="_blank">lucasfip@yahoo.com.br</a>><br>
To: Roman Lu?trik <<a href="mailto:roman.lustrik@biolitika.si" target="_blank">roman.lustrik@biolitika.si</a>><br>
Cc: "<a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge. r-project.org</a>"<br>
<<a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge. r-project.org</a>><br>
Subject: Re: [adegenet-forum] Dots in the DAPC graphic<br>
Message-ID: <<a href="mailto:1994389766.433362.1507809815326@mail.yahoo.com" target="_blank">1994389766.433362. 1507809815326@mail.yahoo.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
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>
Best regards,Lucas Veiga Ayres pimenta<br>
<br>
???Em Quinta-feira, 12 de Outubro de 2017 5:49, Roman Lu?trik <<a href="mailto:roman.lustrik@biolitika.si" target="_blank">roman.lustrik@biolitika.si</a>> escreveu:<br>
<br>
<br>
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>
By default, coloring is done on grouping (see here). See this example:<br>
library(adegenet)<br>
<br>
data(H3N2)<br>
pop(H3N2) <- factor(H3N2$other$epid)<br>
dapc1 <- dapc(H3N2, var.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5)<br>
<br>
data.frame(dapc1$grp, pop(H3N2)) # they are matching<br>
<br>
Cheers,Roman<br>
<br>
<br>
----<br>
In god we trust, all others bring data.<br>
<br>
Zahtevaj IJZ na <a href="https://kurc.biolitika.si/" target="_blank">https://kurc.biolitika.si</a><br>
<br>
From: "Lucas Veiga" <<a href="mailto:lucasfip@yahoo.com.br" target="_blank">lucasfip@yahoo.com.br</a>><br>
To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge. r-project.org</a><br>
Sent: Thursday, October 12, 2017 1:34:19 AM<br>
Subject: [adegenet-forum] Dots in the DAPC graphic<br>
<br>
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>
<br>
Best regards,<br>
Lucas Veiga Ayres Pimenta<br>
______________________________ _________________<br>
adegenet-forum mailing list<br>
<a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge. r-project.org</a><br>
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<br>
------------------------------<br>
<br>
Message: 2<br>
Date: Thu, 12 Oct 2017 12:10:28 +0000 (UTC)<br>
From: Lucas Veiga <<a href="mailto:lucasfip@yahoo.com.br" target="_blank">lucasfip@yahoo.com.br</a>><br>
To: Roman Lu?trik <<a href="mailto:roman.lustrik@biolitika.si" target="_blank">roman.lustrik@biolitika.si</a>><br>
Cc: "<a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge. r-project.org</a>"<br>
<<a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge. r-project.org</a>><br>
Subject: Re: [adegenet-forum] Dots in the DAPC graphic<br>
Message-ID: <<a href="mailto:342879047.415645.1507810228644@mail.yahoo.com" target="_blank">342879047.415645. 1507810228644@mail.yahoo.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
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>
Best regards,Lucas Veiga Ayres pimenta<br>
<br>
???Em Quinta-feira, 12 de Outubro de 2017 9:03, Lucas Veiga <<a href="mailto:lucasfip@yahoo.com.br" target="_blank">lucasfip@yahoo.com.br</a>> escreveu:<br>
<br>
<br>
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>
Best regards,Lucas Veiga Ayres pimenta<br>
<br>
???Em Quinta-feira, 12 de Outubro de 2017 5:49, Roman Lu?trik <<a href="mailto:roman.lustrik@biolitika.si" target="_blank">roman.lustrik@biolitika.si</a>> escreveu:<br>
<br>
<br>
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>
By default, coloring is done on grouping (see here). See this example:<br>
library(adegenet)<br>
<br>
data(H3N2)<br>
pop(H3N2) <- factor(H3N2$other$epid)<br>
dapc1 <- dapc(H3N2, var.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5)<br>
<br>
data.frame(dapc1$grp, pop(H3N2)) # they are matching<br>
<br>
Cheers,Roman<br>
<br>
<br>
----<br>
In god we trust, all others bring data.<br>
<br>
Zahtevaj IJZ na <a href="https://kurc.biolitika.si/" target="_blank">https://kurc.biolitika.si</a><br>
<br>
From: "Lucas Veiga" <<a href="mailto:lucasfip@yahoo.com.br" target="_blank">lucasfip@yahoo.com.br</a>><br>
To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge. r-project.org</a><br>
Sent: Thursday, October 12, 2017 1:34:19 AM<br>
Subject: [adegenet-forum] Dots in the DAPC graphic<br>
<br>
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>
<br>
Best regards,<br>
Lucas Veiga Ayres Pimenta<br>
______________________________ _________________<br>
adegenet-forum mailing list<br>
<a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge. r-project.org</a><br>
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<br>
<br>
<br>
<br>
<br>
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<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Fri, 13 Oct 2017 10:38:57 +0200 (CEST)<br>
From: Roman Lu?trik <<a href="mailto:roman.lustrik@biolitika.si" target="_blank">roman.lustrik@biolitika.si</a>><br>
To: Lucas Veiga <<a href="mailto:lucasfip@yahoo.com.br" target="_blank">lucasfip@yahoo.com.br</a>><br>
Cc: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge. r-project.org</a><br>
Subject: Re: [adegenet-forum] Dots in the DAPC graphic<br>
Message-ID:<br>
<<a href="mailto:181441774.286421.1507883937636.JavaMail.zimbra@biolitika.si" target="_blank">181441774.286421. 1507883937636.JavaMail.zimbra@ biolitika.si</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
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>
<br>
In the mean time, you can construct your own plot, taking bits and pieces from <a href="https://github.com/thibautjombart/adegenet/blob/master/R/dapc.R#L539" target="_blank">
https://github.com/ thibautjombart/adegenet/blob/ master/R/dapc.R#L539</a><br>
<br>
<br>
<br>
Cheers,<br>
Roman<br>
<br>
----<br>
In god we trust, all others bring data.<br>
<br>
Zahtevaj IJZ na <a href="https://kurc.biolitika.si/" target="_blank">https://kurc.biolitika.si</a><br>
<br>
<br>
<br>
From: "Lucas Veiga" <<a href="mailto:lucasfip@yahoo.com.br" target="_blank">lucasfip@yahoo.com.br</a>><br>
To: "Roman Lu?trik" <<a href="mailto:roman.lustrik@biolitika.si" target="_blank">roman.lustrik@biolitika.si</a>><br>
Cc: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge. r-project.org</a><br>
Sent: Thursday, October 12, 2017 2:03:35 PM<br>
Subject: Re: [adegenet-forum] Dots in the DAPC graphic<br>
<br>
Dear Roman,<br>
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>
I hope have explain better my situation and that you can help me.<br>
<br>
Best regards,<br>
Lucas Veiga Ayres pimenta<br>
<br>
<br>
Em Quinta-feira, 12 de Outubro de 2017 5:49, Roman Lu?trik <<a href="mailto:roman.lustrik@biolitika.si" target="_blank">roman.lustrik@biolitika.si</a>> escreveu:<br>
<br>
<br>
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>
By default, coloring is done on grouping ( see here ). See this example:<br>
<br>
library(adegenet)<br>
<br>
data(H3N2)<br>
pop(H3N2) <- factor(H3N2$other$epid)<br>
dapc1 <- dapc(H3N2, var.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5)<br>
<br>
data.frame(dapc1$grp, pop(H3N2)) # they are matching<br>
<br>
Cheers,<br>
Roman<br>
<br>
<br>
<br>
----<br>
In god we trust, all others bring data.<br>
<br>
Zahtevaj IJZ na <a href="https://kurc.biolitika.si/" target="_blank">https://kurc.biolitika.si</a><br>
<br>
<br>
<br>
From: "Lucas Veiga" <<a href="mailto:lucasfip@yahoo.com.br" target="_blank">lucasfip@yahoo.com.br</a>><br>
To: <a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge. r-project.org</a><br>
Sent: Thursday, October 12, 2017 1:34:19 AM<br>
Subject: [adegenet-forum] Dots in the DAPC graphic<br>
<br>
Dear all,<br>
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>
<br>
Best regards,<br>
Lucas Veiga Ayres Pimenta<br>
<br>
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