<div dir="ltr">Hi, <br><br>If you think the individuals you are plotting are spaced far enough that you will be able to read labels at the individual level, one way to do it is to use s.label. <br>Here is an example of how to use s.label to overlap labels to a scatterplot of DAPC:<br><br><div><font color="#6aa84f">#############</font></div><div><font color="#6aa84f">## EXAMPLE ##</font></div><div><font color="#6aa84f">#############</font></div><div><font color="#0000ff">set.seed(14)</font></div><div><font color="#6aa84f"># generate a simulated dataset with 3 populations</font></div><div><font color="#0000ff">simpop <- glSim(100, 500, 5, k=3, sort.pop=TRUE)</font></div><div><font color="#6aa84f"># isolate the SNPs and the population factor</font></div><div><font color="#0000ff">snps <- as.matrix(simpop)</font></div><div><font color="#0000ff">phen <- simpop@other$ancestral.pops</font></div><div><font color="#6aa84f"># run a dapc</font></div><div><font color="#0000ff">dapc1 <- dapc(snps, phen, n.pca=20, n.da=4)</font></div><div><span style="color:rgb(106,168,79)"># create the scatter plot as before</span><font color="#0000ff"><br></font></div><div><font color="#0000ff">scatter(dapc1, cstar=0, cex=5, label=NULL)</font></div><div><font color="#6aa84f"># change graphical parameter to subsequently overlay the labels without drawing a new plot</font></div><div><font color="#0000ff">par(new=TRUE)</font></div><div><font color="#6aa84f"># make a data frame of the dapc coordinates used in scatter</font></div><div><font color="#0000ff">df <- data.frame(x = dapc1$ind.coord[,1], y = dapc1$ind.coord[,2])</font></div><div><font color="#6aa84f"># identify/ create a vector of names for the individuals in your plot</font></div><div><font color="#0000ff">noms <- paste("ind", c(1:100), sep=".")</font></div><div><font color="#6aa84f"># use the text function to add labels to the positions given by the coordinates you used in plot</font></div><div><font color="#0000ff">s.label(dfxy = df, xax=1, yax=2, label=noms, </font></div><div> <font color="#0000ff">clabel=0.7, </font><font color="#6aa84f"># change the size of the labels</font></div><div> <font color="#0000ff">boxes=TRUE,</font> <font color="#6aa84f"># if points are spaced wide enough, can use TRUE to add boxes around the labels</font></div><div> <font color="#0000ff">grid=FALSE, addaxes=FALSE)</font> <font color="#6aa84f"># do not draw lines or axes in addition to the labels</font></div><div><br></div><div><br>The comments in the example above hopefully should give you all of the relevant information, so please give them a read and then feel free to let me know if you have any questions. You will almost certainly want to play around with the arguments clabel and boxes in the s.label function to get the labels to be readable for your case. </div><div>I hope that helps! <br><br>Best, <br>Caitlin. </div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Sep 18, 2014 at 3:08 PM, Maria del Carmen David <span dir="ltr"><<a href="mailto:maria.david.salas@gmail.com" target="_blank">maria.david.salas@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Hello. I can't find the way of labeling individuals in my dapc graphic. I know that for those who work with huge amount of individuals it isn't necessary but i have a bit less than 150 and i want to see how they plot. I have used assignplot to get a better idea of the group assignments but it would be extremely helpful to be able to label my samples. Thanks in advance.<span class="HOEnZb"><font color="#888888"><span style="color:rgb(255,102,0)"></span><br><br></font></span></div><span class="HOEnZb"><font color="#888888">Maria del Carmen<br>
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