[adegenet-forum] Plot supplementary individuals DAPC

Thibaut Jombart thibautjombart at gmail.com
Fri Sep 2 13:11:01 CEST 2016

Dear all,

after some exchanges off the forum (data involved), it turned out there was
indeed a problem: predict.dapc was using raw allele counts and not
frequencies, because of an implicit conversion using as.matrix, which
changed behaviour since version 2.0. This means that all supplementary
individuals were effectively in the right direction, but twice as far from
the origin as they should have been.

I have now fixed this in the devel version (commit b8c29c51).

More importantly: I have recompiled the DAPC tutorial, so that the ugly,
unbearable rainbow colors have now been replaced by the funky palette in
the microbov example. See adegenetTutorial("dapc").

Thanks again to Vanesse for flagging this issue!


Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology
Imperial College London
Twitter: @TeebzR <https://twitter.com/TeebzR>

On 1 September 2016 at 14:07, vlabeyrie <vanesse.labeyrie at cirad.fr> wrote:

> 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
> 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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