[adegenet-forum] Plot supplementary individuals DAPC

[vlabeyrie]

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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