[adegenet-forum] Problem DAPC scatterplot supplementary individuals

[vlabeyrie]

Dear adegenet users,

I have a problem when plotting supplementary individuals on DAPC 
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 African collection individuals
colb<-c("darkblue","dodgerblue","darkorange2","red","gold","grey")  # colors for supplementary Mount Kenya individuals (according to their STRUCTURE group)

#axes 1 and 2
col.points_80<-transp(col[as.integer(pop(x_80))],.2)  # define the color of African 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 / African GCP dataset

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,.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 
full script and data if needed





Thank you for your help !

-- 
Vanesse Labeyrie

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