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<div style="font-size: 14pt;font-family: Arial;"><small><small><span
style="font-family: Arial;">Hi,<br><br>I am trying to get two DAPCs
done:<br>1. a DAPC1 that displays the a priori established groups (in
this case a complex of 5 nominal species) and <br></span></small></small><span><small><small><span
style="font-family: Arial;">2. a DAPC2 that displays the genetic
gorups, with no a priori determination= K clusters<br><br>I have
produced two scatter plots for these two DAPCs which are attached. The
first graph (DAPC1) seems to have a y-axis clear division, and I was
expecting that DAPC2 would display that. But DAPC2 shows a horizontal
grouping.<br><br>Maybe my scripts are not correct. Does anyone can
comment if the code is correct, or am I making some very basic mistakes?<br><br>Many
thanks,<br>Rita<br><br><br><br>The coding I am using is the following:<br></span></small></small></span><small><small><span
style="font-family: Arial;"><br>data.gp <-
read.genepop('infile.gen')<br>#perform temporary DAPC<br>dapc <-
dapc(data.gp, pop=NULL, n.pca=NULL, n.da=NULL)<br>a=optim.a.score(dapc,
n.pca = 1:ncol(dapc$tab), smart=TRUE, n=10, plot=TRUE, n.sim=100,
n.da=length(levels(dapc$grp)))<br>##perform DAPC based on species<br>dapc.species
<- dapc(data.gp, pop=NULL, n.pca=a$best, n.da=NULL, scale=FALSE,
truenames=FALSE, all.contrib=TRUE)<br><<<<<<<<<<<<GRAPH
ON THE LEFT>>>>>>>>>>>>>><br><br>#FIND
CLUSTERS##################################<br>clusters <-
find.clusters(data.gp, choose.n.clust=TRUE,criterion=c("diffNgroup"),
n.pca=a$best,n.clust=NULL, stat='BIC', max.n.clust=10)<br>dapc.clusters<-
dapc(data.gp, grp=clusters$grp, n.pca=a$best)<br><<<<<<<<<<<<GRAPH
ON THE RIGHT>>>>>>>>>>>>>><br><br><br></span></small></small></div>
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