[adegenet-forum] dapc and map

[Sofie Vandewoestijne]

Dear Thibaut Jombart and List members,

I have three questions concerning the mapping of DAPC results:

1) after find.clusters, it appear that individuals from the 5 samples 
sites are genetically grouped into 3 clusters. I would like to map 
this (as in Fig 7, Jombart et al BMC Genetics), but given that I have 
5 localities (xy) and only 3 clusters, isn't it normal that I do not 
have the same number of row numbers in xy and X? (?? dem to post from 
Bernhard Stoeckle??). How do I resolve this error (Erreur dans 
colorplot.default(xy, -dapc.a$grp.coord, cex = 3, add = TRUE,  :
   xy and X have different row numbers) ?

 > dim(xy)
[1] 5 2
 > dim(dapc.a$grp.coord)
[1] 3 2

 > if(require(maps)){
+
+ xy <- cbind(data$other$popInfo$Longitude, data$other$popInfo$Latitude)
+
+ par(mar=rep(.1,4))
+ map(fill=TRUE, col="lightgrey")
+ colorplot(xy, -dapc.a$grp.coord, cex=3, add=TRUE, trans=FALSE)
+ }
Erreur dans colorplot.default(xy, -dapc.a$grp.coord, cex = 3, add = TRUE,  :
   xy and X have different row numbers

2) where can one download maps from countries other than those 
provided in the map package?

3) finally, when there are 2 BIC values that are very similar, should 
one choose for the smaller number of clusters even if it has a higher 
BIC value?

Thank you for your help!

Sincerely yours,

Sofie

Sofie Vandewoestijne
Postdoctoral fellow
Biodiversity Research Centre
Catholic University Louvain
Place Croix du Sud 5
B-1348 Louvain-la-Neuve
Belgium

Tel: 32 (0)10 473454
Fax: 32 (0)10 473490

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