<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_1508843118552_20625"><span id="yui_3_16_0_ym19_1_1508843118552_20626">Oliver, sorry my delay.<br>I solved my problem with this command:<br><br></span></div><div id="yui_3_16_0_ym19_1_1508843118552_20627">mycol = c("darkblue","black","red")</div><div id="yui_3_16_0_ym19_1_1508843118552_20628">#### s.class(dapc_cerato$ind.coord, pop(cerato), pch = 18, cstar=1, cellipse=0.95, cpoint=1, clabel = 0.6, grid=FALSE, xlim=NULL, ylim=NULL, origin = c(0,0), axesell=FALSE, addaxes=TRUE, col = mycol)</div><div dir="ltr" id="yui_3_16_0_ym19_1_1508843118552_20629">####legend(xy.coords(x = c(-30,10), y = c(24,-10)), pch=19, cex=1.5, pt.cex=1.5,bty="n", levels(pop(cerato)), ncol=6, y.intersp=0.5, x.intersp=0.5, col= seasun(length(levels(dapc_cerato$grp))))</div><div id="yui_3_16_0_ym19_1_1508843118552_20630"><span><br></span></div><div id="yui_3_16_0_ym19_1_1508843118552_20303" dir="ltr"><span id="yui_3_16_0_ym19_1_1508843118552_21542">The result is in the attached file.<br><br>Best regards,<br>Lucas Veiga Ayres Pimenta</span></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 Quarta-feira, 18 de Outubro de 2017 22:39, "Oliver.Berry@csiro.au" <Oliver.Berry@csiro.au> escreveu:<br></font></div> <br><br> <div class="y_msg_container"><div id="yiv0717832304"><style>#yiv0717832304 #yiv0717832304 --
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<div class="yiv0717832304MsoNormal"><span style="font-size:14.0pt;">Hi,</span></div>
<div class="yiv0717832304MsoNormal"><span style="font-size:14.0pt;"> </span></div>
<div class="yiv0717832304MsoNormal"><span style="font-size:14.0pt;">That’s great news Lucas.</span></div>
<div class="yiv0717832304MsoNormal"><span style="font-size:14.0pt;"> </span></div>
<div class="yiv0717832304MsoNormal"><span style="font-size:14.0pt;">I wonder whether you would mind posting a version of your solution so others can make use of it in the future?</span></div>
<div class="yiv0717832304MsoNormal"><span style="font-size:14.0pt;"> </span></div>
<div class="yiv0717832304MsoNormal"><span style="font-size:14.0pt;">Cheers,</span></div>
<div class="yiv0717832304MsoNormal"><span style="font-size:14.0pt;"> </span></div>
<div class="yiv0717832304MsoNormal"><span style="font-size:14.0pt;">Olly</span></div>
<div class="yiv0717832304MsoNormal"><span style="font-size:14.0pt;"> </span></div>
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<div class="yiv0717832304MsoNormal" style="line-height:115%;">
<b><span style="font-size:10.0pt;line-height:115%;">Oliver Berry</span></b></div>
<div class="yiv0717832304MsoNormal" style="line-height:115%;">
<span style="font-size:10.0pt;line-height:115%;">Leader, Environomics Future Science Platform</span></div>
<div class="yiv0717832304MsoNormal" style="line-height:115%;">
<span style="font-size:10.0pt;line-height:115%;">CSIRO National Collections and Marine Infrastructure</span></div>
<div class="yiv0717832304MsoNormal"><span style="font-size:9.0pt;">Indian Ocean Marine Research Centre</span></div>
<div class="yiv0717832304MsoNormal"><span style="font-size:9.0pt;">The University of Western Australia, M097, 35 Stirling Highway</span></div>
<div class="yiv0717832304MsoNormal"><span style="font-size:9.0pt;">Crawley, W.A., 6009, Australia
</span></div>
<div class="yiv0717832304MsoNormal" style="line-height:115%;">
<b><span style="font-size:10.0pt;line-height:115%;">P</span></b><span style="font-size:10.0pt;line-height:115%;">: +61-8-9333-6584
<b>F: </b>+61-8-9333-6555</span><span style="font-size:10.0pt;line-height:115%;">
</span><b><span style="font-size:10.0pt;line-height:115%;">E</span></b><span style="font-size:10.0pt;line-height:115%;">:
<a rel="nofollow" shape="rect" ymailto="mailto:Oliver.Berry@csiro.au" target="_blank" href="mailto:Oliver.Berry@csiro.au">Oliver.Berry@csiro.au</a> <b>W</b>: </span>
<span style="font-size:10.0pt;line-height:115%;"><a rel="nofollow" shape="rect" target="_blank" href="https://research.csiro.au/environomics/">Environomics</a></span><u><span style="font-size:10.0pt;line-height:115%;"></span></u></div>
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<div class="yiv0717832304MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;">From:</span></b><span lang="EN-US" style="font-size:11.0pt;"> Lucas Veiga [mailto:lucasfip@yahoo.com.br]
<br clear="none">
<b>Sent:</b> Thursday, 19 October 2017 7:55 AM<br clear="none">
<b>To:</b> adegenet-forum@lists.r-forge.r-project.org; Berry, Olly (NCMI, IOMRC Crawley) <Oliver.Berry@csiro.au><br clear="none">
<b>Subject:</b> Re: [adegenet-forum] Dots in the DAPC graphic (Lucas Veiga)</span></div>
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<div class="yiv0717832304MsoNormal" style="margin-bottom:12.0pt;background:white;"><span style="font-size:10.0pt;color:black;">Dear all,<br clear="none" id="yiv0717832304yui_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 clear="none" id="yiv0717832304yui_3_16_0_ym19_1_1508369539247_14598">
<br clear="none" id="yiv0717832304yui_3_16_0_ym19_1_1508369539247_14599">
Best regards,<br clear="none" id="yiv0717832304yui_3_16_0_ym19_1_1508369539247_14600">
Lucas Veiga Ayres Pimenta</span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="font-size:10.0pt;">Em Terça-feira, 17 de Outubro de 2017 8:23, Shannon O'Leary <<a rel="nofollow" shape="rect" ymailto="mailto:shannon.j.oleary@gmail.com" target="_blank" href="mailto:shannon.j.oleary@gmail.com">shannon.j.oleary@gmail.com</a>>
escreveu:</span><span style=""></span></div>
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<div class="yiv0717832304MsoNormal" style="margin-bottom:12.0pt;background:white;"><span style=""> </span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">Hi Lucas,</span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">Try this on for size: </span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">From your description it looks like you have a data set for which you have the following information:</span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">SAMPLE-ID | POPULATION (CROP) | GENOTYPES</span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
</div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">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)</span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">You then ran k-means clustering/DAPC on your data set, something like this</span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">grp <- find.clusters.genind(gen, n.pca = 200,</span></div>
</div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> stat = "BIC", choose.n.clust = FALSE, criterion = "min",</span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> max.n.clust = 40)</span></div>
</div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">dapc <-dapc(gen, grp$grp, n.pca = 50, n.da = 2)</span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">You can pull the information on which sample was assigned to which cluster like so:</span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
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<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">clusters <- as.data.frame(grp$grp) %>%</span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> rownames_to_column("SAMPLE_ID") %>%</span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> rename(CLUSTER = `grp$grp`)</span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">You can add this information to your SampleInfo dataframe using dplyr::left_join()</span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">SampleInfo <- left_join(SampleInfo, clusters, by = "SAMPLE_ID")</span></div>
</div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">resulting in a dataframe with 3 columns: SAMPLE_ID | CROP | CLUSTER.</span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
</div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">Now you can pull the coordinates from the dapc and also add them to that data frame as well:</span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
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<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">DAPC_Ind <- as.data.frame(dapc$ind.coord) %>%</span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> rownames_to_column("SAMPLE_ID")</span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
</div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">SampleInfo <- left_join(SampleInfo, DAPC_Ind, by = "SAMPLE_ID")</span></div>
</div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">Now you have a data frame that should look something like this</span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">SAMPLE_ID | CROP | CLUSTER | LD1 | LD2 ...</span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">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:</span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">ggplot(SampleInfo, aes(x = LD1, y = LD2), color = CROP, shape = CLUSTER) +</span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">geom_point()</span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">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).</span></div>
</div>
<div>
<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
</div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style=""> </span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">Shannon</span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="font-size:7.5pt;">><(((jº> ><(((jº> ><(((jº> ><(((jº> </span><span style="font-size:10.0pt;">><(((jº> ><(((jº>
><(((jº> </span><span style=""></span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="font-size:9.5pt;">Shannon J. O'Leary</span><span style=""></span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">Postdoctoral Research Associate</span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">Marine Genomics Lab</span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">Life Science Department</span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">Texas A&M Corpus Christi</span></div>
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<div class="yiv0717832304MsoNormal" style="background:white;"><span style="">On Mon, Oct 16, 2017 at 12:11 PM, <<a rel="nofollow" shape="rect" ymailto="mailto:adegenet-forum-request@lists.r-forge.r-project.org" target="_blank" href="mailto:adegenet-forum-request@lists.r-forge.r-project.org">adegenet-forum-request@lists.r-forge.r-project.org</a>>
wrote:</span></div>
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1. Re: Dots in the DAPC graphic (Lucas Veiga)<br clear="none">
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Message: 1<br clear="none">
Date: Mon, 16 Oct 2017 17:10:49 +0000 (UTC)<br clear="none">
From: Lucas Veiga <<a rel="nofollow" shape="rect" ymailto="mailto:lucasfip@yahoo.com.br" target="_blank" href="mailto:lucasfip@yahoo.com.br">lucasfip@yahoo.com.br</a>><br clear="none">
To: Zhian Kamvar <<a rel="nofollow" shape="rect" ymailto="mailto:zkamvar@gmail.com" target="_blank" href="mailto:zkamvar@gmail.com">zkamvar@gmail.com</a>>,<br clear="none">
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Subject: Re: [adegenet-forum] Dots in the DAPC graphic<br clear="none">
Message-ID: <<a rel="nofollow" shape="rect" ymailto="mailto:1729769391.894921.1508173849615@mail.yahoo.com" target="_blank" href="mailto:1729769391.894921.1508173849615@mail.yahoo.com">1729769391.894921. 1508173849615@mail.yahoo.com</a>><br clear="none">
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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 clear="none">
<br clear="none">
Best regards,Lucas Veiga Ayres Pimenta<br clear="none">
<br clear="none">
Em Sexta-feira, 13 de Outubro de 2017 12:48, Zhian Kamvar <<a rel="nofollow" shape="rect" ymailto="mailto:zkamvar@gmail.com" target="_blank" href="mailto:zkamvar@gmail.com">zkamvar@gmail.com</a>> escreveu:<br clear="none">
<br clear="none">
<br clear="none">
Hi,<br clear="none">
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 clear="none">
I have recently come up with a ggplot2 solution for this:?<a rel="nofollow" shape="rect" target="_blank" href="https://github.com/everhartlab/sclerotinia-366/blame/v1.0/results/by-year.md#L508-L558">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" shape="rect" target="_blank" href="https://github.com/everhartlab/sclerotinia-366/blob/v1.0/results/figures/by-year/dapc_plot-2.png">https://github.com/ everhartlab/sclerotinia-366/ blob/v1.0/results/figures/by- year/dapc_plot-2.png</a><br clear="none">
Hope that helps,Zhian<br clear="none">
-----Zhian N. Kamvar, Ph. D.Postdoctoral Researcher (Everhart Lab)Department of Plant PathologyUniversity of Nebraska-LincolnORCID:?0000- 0003-1458-7108<br clear="none">
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On Oct 13, 2017, at 03:39 , <a rel="nofollow" shape="rect" ymailto="mailto:adegenet-forum-request@lists.r-forge.r-project.org" target="_blank" href="mailto:adegenet-forum-request@lists.r-forge.r-project.org">
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??1. Re: Dots in the DAPC graphic (Lucas Veiga)<br clear="none">
??2. Re: Dots in the DAPC graphic (Lucas Veiga)<br clear="none">
??3. Re: Dots in the DAPC graphic (Roman Lu?trik)<br clear="none">
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Message: 1<br clear="none">
Date: Thu, 12 Oct 2017 12:03:35 +0000 (UTC)<br clear="none">
From: Lucas Veiga <<a rel="nofollow" shape="rect" ymailto="mailto:lucasfip@yahoo.com.br" target="_blank" href="mailto:lucasfip@yahoo.com.br">lucasfip@yahoo.com.br</a>><br clear="none">
To: Roman Lu?trik <<a rel="nofollow" shape="rect" ymailto="mailto:roman.lustrik@biolitika.si" target="_blank" href="mailto:roman.lustrik@biolitika.si">roman.lustrik@biolitika.si</a>><br clear="none">
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Subject: Re: [adegenet-forum] Dots in the DAPC graphic<br clear="none">
Message-ID: <<a rel="nofollow" shape="rect" ymailto="mailto:1994389766.433362.1507809815326@mail.yahoo.com" target="_blank" href="mailto:1994389766.433362.1507809815326@mail.yahoo.com">1994389766.433362. 1507809815326@mail.yahoo.com</a>><br clear="none">
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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 clear="none">
Best regards,Lucas Veiga Ayres pimenta<br clear="none">
<br clear="none">
???Em Quinta-feira, 12 de Outubro de 2017 5:49, Roman Lu?trik <<a rel="nofollow" shape="rect" ymailto="mailto:roman.lustrik@biolitika.si" target="_blank" href="mailto:roman.lustrik@biolitika.si">roman.lustrik@biolitika.si</a>> escreveu:<br clear="none">
<br clear="none">
<br clear="none">
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 clear="none">
By default, coloring is done on grouping (see here). See this example:<br clear="none">
library(adegenet)<br clear="none">
<br clear="none">
data(H3N2)<br clear="none">
pop(H3N2) <- factor(H3N2$other$epid)<br clear="none">
dapc1 <- dapc(H3N2, var.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5)<br clear="none">
<br clear="none">
data.frame(dapc1$grp, pop(H3N2)) # they are matching<br clear="none">
<br clear="none">
Cheers,Roman<br clear="none">
<br clear="none">
<br clear="none">
----<br clear="none">
In god we trust, all others bring data.<br clear="none">
<br clear="none">
Zahtevaj IJZ na <a rel="nofollow" shape="rect" target="_blank" href="https://kurc.biolitika.si/">https://kurc.biolitika.si</a><br clear="none">
<br clear="none">
From: "Lucas Veiga" <<a rel="nofollow" shape="rect" ymailto="mailto:lucasfip@yahoo.com.br" target="_blank" href="mailto:lucasfip@yahoo.com.br">lucasfip@yahoo.com.br</a>><br clear="none">
To: <a rel="nofollow" shape="rect" ymailto="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank" href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge. r-project.org</a><br clear="none">
Sent: Thursday, October 12, 2017 1:34:19 AM<br clear="none">
Subject: [adegenet-forum] Dots in the DAPC graphic<br clear="none">
<br clear="none">
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 clear="none">
<br clear="none">
Best regards,<br clear="none">
Lucas Veiga Ayres Pimenta<br clear="none">
______________________________ _________________<br clear="none">
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Date: Thu, 12 Oct 2017 12:10:28 +0000 (UTC)<br clear="none">
From: Lucas Veiga <<a rel="nofollow" shape="rect" ymailto="mailto:lucasfip@yahoo.com.br" target="_blank" href="mailto:lucasfip@yahoo.com.br">lucasfip@yahoo.com.br</a>><br clear="none">
To: Roman Lu?trik <<a rel="nofollow" shape="rect" ymailto="mailto:roman.lustrik@biolitika.si" target="_blank" href="mailto:roman.lustrik@biolitika.si">roman.lustrik@biolitika.si</a>><br clear="none">
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Subject: Re: [adegenet-forum] Dots in the DAPC graphic<br clear="none">
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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 clear="none">
Best regards,Lucas Veiga Ayres pimenta<br clear="none">
<br clear="none">
???Em Quinta-feira, 12 de Outubro de 2017 9:03, Lucas Veiga <<a rel="nofollow" shape="rect" ymailto="mailto:lucasfip@yahoo.com.br" target="_blank" href="mailto:lucasfip@yahoo.com.br">lucasfip@yahoo.com.br</a>> escreveu:<br clear="none">
<br clear="none">
<br clear="none">
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 clear="none">
Best regards,Lucas Veiga Ayres pimenta<br clear="none">
<br clear="none">
???Em Quinta-feira, 12 de Outubro de 2017 5:49, Roman Lu?trik <<a rel="nofollow" shape="rect" ymailto="mailto:roman.lustrik@biolitika.si" target="_blank" href="mailto:roman.lustrik@biolitika.si">roman.lustrik@biolitika.si</a>> escreveu:<br clear="none">
<br clear="none">
<br clear="none">
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 clear="none">
By default, coloring is done on grouping (see here). See this example:<br clear="none">
library(adegenet)<br clear="none">
<br clear="none">
data(H3N2)<br clear="none">
pop(H3N2) <- factor(H3N2$other$epid)<br clear="none">
dapc1 <- dapc(H3N2, var.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5)<br clear="none">
<br clear="none">
data.frame(dapc1$grp, pop(H3N2)) # they are matching<br clear="none">
<br clear="none">
Cheers,Roman<br clear="none">
<br clear="none">
<br clear="none">
----<br clear="none">
In god we trust, all others bring data.<br clear="none">
<br clear="none">
Zahtevaj IJZ na <a rel="nofollow" shape="rect" target="_blank" href="https://kurc.biolitika.si/">https://kurc.biolitika.si</a><br clear="none">
<br clear="none">
From: "Lucas Veiga" <<a rel="nofollow" shape="rect" ymailto="mailto:lucasfip@yahoo.com.br" target="_blank" href="mailto:lucasfip@yahoo.com.br">lucasfip@yahoo.com.br</a>><br clear="none">
To: <a rel="nofollow" shape="rect" ymailto="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank" href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge. r-project.org</a><br clear="none">
Sent: Thursday, October 12, 2017 1:34:19 AM<br clear="none">
Subject: [adegenet-forum] Dots in the DAPC graphic<br clear="none">
<br clear="none">
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 clear="none">
<br clear="none">
Best regards,<br clear="none">
Lucas Veiga Ayres Pimenta<br clear="none">
______________________________ _________________<br clear="none">
adegenet-forum mailing list<br clear="none">
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Message: 3<br clear="none">
Date: Fri, 13 Oct 2017 10:38:57 +0200 (CEST)<br clear="none">
From: Roman Lu?trik <<a rel="nofollow" shape="rect" ymailto="mailto:roman.lustrik@biolitika.si" target="_blank" href="mailto:roman.lustrik@biolitika.si">roman.lustrik@biolitika.si</a>><br clear="none">
To: Lucas Veiga <<a rel="nofollow" shape="rect" ymailto="mailto:lucasfip@yahoo.com.br" target="_blank" href="mailto:lucasfip@yahoo.com.br">lucasfip@yahoo.com.br</a>><br clear="none">
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Subject: Re: [adegenet-forum] Dots in the DAPC graphic<br clear="none">
Message-ID:<br clear="none">
<<a rel="nofollow" shape="rect" ymailto="mailto:181441774.286421.1507883937636.JavaMail.zimbra@biolitika.si" target="_blank" href="mailto:181441774.286421.1507883937636.JavaMail.zimbra@biolitika.si">181441774.286421. 1507883937636.JavaMail.zimbra@ biolitika.si</a>><br clear="none">
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<br clear="none">
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 clear="none">
<br clear="none">
In the mean time, you can construct your own plot, taking bits and pieces from <a rel="nofollow" shape="rect" target="_blank" href="https://github.com/thibautjombart/adegenet/blob/master/R/dapc.R#L539">
https://github.com/ thibautjombart/adegenet/blob/ master/R/dapc.R#L539</a><br clear="none">
<br clear="none">
<br clear="none">
<br clear="none">
Cheers,<br clear="none">
Roman<br clear="none">
<br clear="none">
----<br clear="none">
In god we trust, all others bring data.<br clear="none">
<br clear="none">
Zahtevaj IJZ na <a rel="nofollow" shape="rect" target="_blank" href="https://kurc.biolitika.si/">https://kurc.biolitika.si</a><br clear="none">
<br clear="none">
<br clear="none">
<br clear="none">
From: "Lucas Veiga" <<a rel="nofollow" shape="rect" ymailto="mailto:lucasfip@yahoo.com.br" target="_blank" href="mailto:lucasfip@yahoo.com.br">lucasfip@yahoo.com.br</a>><br clear="none">
To: "Roman Lu?trik" <<a rel="nofollow" shape="rect" ymailto="mailto:roman.lustrik@biolitika.si" target="_blank" href="mailto:roman.lustrik@biolitika.si">roman.lustrik@biolitika.si</a>><br clear="none">
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Sent: Thursday, October 12, 2017 2:03:35 PM<br clear="none">
Subject: Re: [adegenet-forum] Dots in the DAPC graphic<br clear="none">
<br clear="none">
Dear Roman,<br clear="none">
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 clear="none">
I hope have explain better my situation and that you can help me.<br clear="none">
<br clear="none">
Best regards,<br clear="none">
Lucas Veiga Ayres pimenta<br clear="none">
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Em Quinta-feira, 12 de Outubro de 2017 5:49, Roman Lu?trik <<a rel="nofollow" shape="rect" ymailto="mailto:roman.lustrik@biolitika.si" target="_blank" href="mailto:roman.lustrik@biolitika.si">roman.lustrik@biolitika.si</a>> escreveu:<br clear="none">
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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 clear="none">
By default, coloring is done on grouping ( see here ). See this example:<br clear="none">
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library(adegenet)<br clear="none">
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data(H3N2)<br clear="none">
pop(H3N2) <- factor(H3N2$other$epid)<br clear="none">
dapc1 <- dapc(H3N2, var.contrib=FALSE, scale=FALSE, n.pca=150, n.da=5)<br clear="none">
<br clear="none">
data.frame(dapc1$grp, pop(H3N2)) # they are matching<br clear="none">
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Cheers,<br clear="none">
Roman<br clear="none">
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<br clear="none">
<br clear="none">
----<br clear="none">
In god we trust, all others bring data.<br clear="none">
<br clear="none">
Zahtevaj IJZ na <a rel="nofollow" shape="rect" target="_blank" href="https://kurc.biolitika.si/">https://kurc.biolitika.si</a><br clear="none">
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From: "Lucas Veiga" <<a rel="nofollow" shape="rect" ymailto="mailto:lucasfip@yahoo.com.br" target="_blank" href="mailto:lucasfip@yahoo.com.br">lucasfip@yahoo.com.br</a>><br clear="none">
To: <a rel="nofollow" shape="rect" ymailto="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank" href="mailto:adegenet-forum@lists.r-forge.r-project.org">adegenet-forum@lists.r-forge. r-project.org</a><br clear="none">
Sent: Thursday, October 12, 2017 1:34:19 AM<br clear="none">
Subject: [adegenet-forum] Dots in the DAPC graphic<br clear="none">
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Dear all,<br clear="none">
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 clear="none">
<br clear="none">
Best regards,<br clear="none">
Lucas Veiga Ayres Pimenta<br clear="none">
<br clear="none">
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