<html><body><div style="font-family: trebuchet ms,sans-serif; font-size: 12pt; color: #000000"><div>Max is asking on how to remove the labels.</div><div><br data-mce-bogus="1"></div><div>This example was taken from the adegenet vignette (<a href="http://adegenet.r-forge.r-project.org/files/tutorial-basics.pdf" data-mce-href="http://adegenet.r-forge.r-project.org/files/tutorial-basics.pdf">see page 57</a>) and it gets you pretty close to what you want.</div><div><br data-mce-bogus="1"></div><div style="padding-left: 30px;"><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;">library(adegenet)</span><br><br><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;">data(microbov)</span><br><br><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;">mb <- scaleGen(microbov, NA.method = "mean")</span><br><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;">pca.cows <- dudi.pca(mb, center = FALSE, scale = FALSE, scannf = FALSE, nf = 3)</span><br><br><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;">par(mfrow = c(2, 1))</span><br><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;">s.class(pca.cows$li, pop(microbov), </span><br><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> xax = 1, yax = 3, col = transp(funky(15), .6), axesell=FALSE,</span><br><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;"> cstar=0, cpoint=3, grid=FALSE)</span><br><br><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;">colorplot(pca.cows$li[c(1,3)], pca.cows$li, transp=TRUE, cex=3, xlab="PC 1", ylab="PC 3")</span><br><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;">title("PCA of microbov dataset\naxes 1-3")</span><br><span style="font-family: "courier new", courier, monaco, monospace, sans-serif;" data-mce-style="font-family: 'courier new', courier, monaco, monospace, sans-serif;">abline(v=0,h=0,col="grey", lty=2)</span></div><div><br data-mce-bogus="1"></div><div><br data-mce-bogus="1"></div><div><br data-mce-bogus="1"></div><div>Cheers,</div><div>Roman</div><div><br></div><div data-marker="__SIG_PRE__">----<br>In god we trust, all others bring data.</div><br><hr id="zwchr" data-marker="__DIVIDER__"><div data-marker="__HEADERS__"><b>From: </b>"mw14533 2014" <mw14533.2014@my.bristol.ac.uk><br><b>To: </b>"Roman Luštrik" <roman.lustrik@biolitika.si><br><b>Sent: </b>Thursday, November 24, 2016 9:39:45 AM<br><b>Subject: </b>Re: [adegenet-forum] PCoA<br></div><br><div data-marker="__QUOTED_TEXT__"><div dir="ltr"><div>Hello Roman<br><br></div><div>The question i meant to ask was how do i remove the labels from the graph? sorry i seem to have been quite unhelpful and forgot to put that in my initial email.<br><br></div><div>Many thanks<br></div><div>Max<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Nov 24, 2016 at 7:48 AM, Roman Luštrik <span dir="ltr"><<a href="mailto:roman.lustrik@biolitika.si" target="_blank">roman.lustrik@biolitika.si</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0 0 0 .8ex; border-left: 1px #ccc solid; padding-left: 1ex;" data-mce-style="margin: 0 0 0 .8ex; border-left: 1px #ccc solid; padding-left: 1ex;"><div><div style="font-family: trebuchet ms,sans-serif; font-size: 12pt; color: #000000;" data-mce-style="font-family: trebuchet ms,sans-serif; font-size: 12pt; color: #000000;"><div>Hello Max,</div><br><div>is there a question here? If you have problems with your code, it's best to provide a reproducible example. Feel free to use any of the datasets that comes shipped with adegenet or perhaps you could simulate your own data.</div><br><div>Cheers,</div><div>Roman</div><br><div>----<br>In god we trust, all others bring data.</div><br><hr id="m_-3304653415294958291zwchr"><div><b>From: </b>"Max Williams" <<a href="mailto:mw14533.2014@my.bristol.ac.uk" target="_blank">mw14533.2014@my.bristol.ac.uk</a>><br><b>To: </b><a href="mailto:adegenet-forum@lists.r-forge.r-project.org" target="_blank">adegenet-forum@lists.r-forge.r-project.org</a><br><b>Sent: </b>Wednesday, November 23, 2016 9:05:17 PM<br><b>Subject: </b>[adegenet-forum] PCoA<br></div><br><div><div><div class="h5"><div dir="ltr"><div><div><div>Dear All<br><br></div>I have recently used PCoA in adegenet to produce the following graph, using the s.class function (shown in attachment). Once i defined my PCoA data as the variable "pca.kelp" i inputted this into adegenet:<br><br>s.class(pca.cows$li, fac=pop(microbov), col=funky(15))<br><br></div>s.class(pca.kelp$li, fac=pop(genind1), <br> +col=transp(funky(15),.6),<br></div> +axesel=FALSE, cstar=0, cpoint=3)<br><div><br><div>I am fairly new to R statistics and would appreciate your time.<br><br></div><div>Many thanks<br></div><div>Max<br></div></div></div>
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