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Good Morning,
<div class=""> I must be missing something about an old thread (<i class="">Fri Aug 8 11:54:08 CEST 2014)</i> that appears to have a solution, but does not work for me.</div>
<div class="">To restate the problem: I want to color individuals by population, but keep the optimal DAPC clusters.</div>
<div class="">My data (CR_84) has 84 individuals from 6 “populations" with 3,243 SNPs, BIC suggest 3 clusters.</div>
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<div class="">CR_84 is a GENLIGHT OBJECT </div>
<div class=""> // 84 genotypes, 3,243 binary SNPs, size: 504.5 Kb</div>
<div class=""> 28119 (0.1 %) missing data</div>
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<div class=""> // Basic content</div>
<div class=""> @gen: list of 84 SNPbin</div>
<div class=""> @ploidy: ploidy of each individual (range: 2-2)</div>
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<div class=""> // Optional content</div>
<div class=""> @ind.names: 84 individual labels</div>
<div class=""> @loc.names: 3243 locus labels</div>
<div class=""> @pop: population of each individual (group size range: 4-22)</div>
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<div class="">If I follow the previous advice (<i class="">Fri Aug 8 11:54:08 CEST 2014) </i>I get two different plots one that has the 3 groups colored by group and the 2nd is 6 groups colored by pop.</div>
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<div class="">#make a DAPC - this uses by optimum DAPC</div>
<div class="">dapc1 <- dapc(CR_84, n.pca=7, n.da=5, grp$grp)</div>
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<div class=""># plot with groups used in DAPC</div>
<div class="">scatter(dapc1)</div>
<div class="">## I get a scatter plot with 3 groups where 2 of the groups have individuals from 5 “populations” that has 3 colors (by group)</div>
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<div class=""># plot with another group - the species — “species" was from the toy data set: microbov$other$spe </div>
<div class=""># I used "grp=CR_84$pop"</div>
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<div class="">scatter(dapc1, grp=CR_84$pop)</div>
<div class="">## I get a scatter plot with 6 groups where 5 of the groups are scatter together. </div>
<div class="">##That is, I do not get the three groups with individuals colored by populations. </div>
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<div class="">What am I missing here? </div>
<div class="">Any clarification would be great.</div>
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<div class="">Cheers</div>
<div class="">Douglas</div>
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——************________*********————</div>
<div style="color: rgb(0, 0, 0); font-family: Georgia; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Douglas L. Crawford<br class="">
Professor, Marine Biology & Ecology<br class="">
Rosenstiel School of Marine & Atmospheric Science<br class="">
University of Miami<br class="">
4600 Rickenbacker Causeway<br class="">
Mami, FL 33149<br class="">
305-421-4121<br class="">
<br class="">
<a href="mailto:dcrawford@miami.edu" class="">dcrawford@miami.edu</a><br class="">
http://www.funhe-evol.org/<br class="">
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