[adegenet-forum] Plot supplementary individuals DAPC
vanesse.labeyrie at cirad.fr
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
I defined two datasets: 1 to perform DAPC and another of supplementary
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
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
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
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 groups
col.sup_80<-colb[as.integer(pop(x.sup_80))] ## Define supplementary
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 !
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