Thu Sep 1 15:07:08 CEST 2016

```Dear adegenet users,

I have a problem when plotting supplementary individuals on DAPC
scatterplot: while they are clearly assigned to a group (with a very
high probability), they are displayed outside of this group on the
scatterplot.

I defined two datasets: 1 to perform DAPC and another of supplementary
individuals

x.sup_80<-Ge_atp_gcp_80[c(1:nrow(Ge_atp at tab)),] # supplementary individuals

x_80<-Ge_atp_gcp_80[-c(1:nrow(Ge_atp at tab)),] # Individuals on which
performing DAPC

Then I performed DAPC on X_80, specifying a-priori groups

dapc_GCP_14ssr_STRk5_b<- dapc(x_80, pop(x_80), n.pca=30,n.da=4) #perform
DAPC

I assigned supplementary individuals to DAPC groups

predict_atp_strk5<-predict.dapc(dapc_GCP_14ssr_STRk5_b,newdata=x.sup_80

The predicted group memberships of supplementary individuals based on
DAPC results is high, so I expect that supplementary individuals would
be located in the DAPC groups  ...

But it is not the case, as on the scatterplot, supplementary individuals
mostly appear outside from the groups to which they are assigned  !!

col<-c("#F8766D", "#A3A500", "#00BF7D", "#00B0F6", "#E76BF3") # colors
for DAPC individuals
colb<-c("darkblue","dodgerblue","darkorange2","red","gold","grey") #
colors for supplementary  individuals

#axes 1 and 2
col.points_80<-transp(col[as.integer(pop(x_80))],.2) # define the color
of DAPC individuals as transparent
scatter(dapc_GCP_14ssr_STRk5_b,col=col,bg="white",scree.da=0,pch="",cstar=0,clab=0,xlim=c(-10,10),legend=F)#

par(xpd=TRUE)
points(dapc_GCP_14ssr_STRk5_b\$ind.coord[,1],
dapc_GCP_14ssr_STRk5_b\$ind.coord[,2],pch=20,col=col.points_80,cex=1) ##
scatter DAPC groups

col.sup_80<-colb[as.integer(pop(x.sup_80))] ## Define supplementary
individuals color
points(predict_atp_strk5\$ind.scores[,1],
predict_atp_strk5\$ind.scores[,2],pch=8,col=transp(col.sup_80,<
span class="number" style="box-sizing: border-box; color: rgb(0, 153,
153);">.7),cex=1) # plot supplementary individuals

With a previous version of adegenet, this problem did not appear as
supplementary individuals were located within the DAPC groups, and this
problem appeared while running my script with the new adegenet version ...

Does someone have an idea of what the problem is ? I can provide the
picture of the scatterplot, full script and data if needed

Thank you for your help !

--
Vanesse Labeyrie

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