[adegenet-forum] DAPC scatter plot and individual colour by population

[Crawford, Douglas L]

Good Morning,
      I must be missing something about an old thread (Fri Aug 8 11:54:08 CEST 2014) that appears to have a solution, but does not work for me.
To restate the problem:  I want to color individuals by population, but keep the optimal DAPC clusters.
My data (CR_84) has 84 individuals from 6 “populations" with 3,243 SNPs, BIC suggest 3 clusters.
CR_84 is  a GENLIGHT OBJECT
 // 84 genotypes,  3,243 binary SNPs, size: 504.5 Kb
 28119 (0.1 %) missing data

 // Basic content
   @gen: list of 84 SNPbin
   @ploidy: ploidy of each individual  (range: 2-2)

 // Optional content
   @ind.names:  84 individual labels
   @loc.names:  3243 locus labels
   @pop: population of each individual (group size range: 4-22)

If I follow the previous advice (Fri Aug 8 11:54:08 CEST 2014)  I get two different plots one that has the 3 groups colored by group and the 2nd is 6 groups colored by pop.

#make a DAPC - this uses by optimum DAPC
dapc1 <- dapc(CR_84, n.pca=7, n.da=5, grp$grp)

# plot with groups used in DAPC
scatter(dapc1)
## I get a scatter plot with 3 groups where 2 of the groups have individuals from 5 “populations” that has 3 colors (by group)

# plot with another group - the species  — “species" was from the toy data set:  microbov$other$spe
# I used "grp=CR_84$pop"

scatter(dapc1, grp=CR_84$pop)
## I get a scatter plot with 6 groups where 5 of the groups are scatter together.
##That is, I do not get the three groups with individuals colored by populations.

What am I missing here?
Any clarification would be great.

Cheers
Douglas


——************________*********————
Douglas L. Crawford
Professor, Marine Biology & Ecology
Rosenstiel School of Marine & Atmospheric Science
University of Miami
4600 Rickenbacker Causeway
Mami, FL 33149
305-421-4121

dcrawford at miami.edu<mailto:dcrawford at miami.edu>
http://www.funhe-evol.org/


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