[adegenet-forum] DAPC

Markus Ruhsam M.Ruhsam at rbge.ac.uk
Thu May 8 13:10:22 CEST 2014


It's the first time I am using DAPC to analyse my data and have the following question. Is it correct that in the plot generated by the scatter function samples are coloured according to their k-means group membership and not according to their DAPC membership probability? If this is right is there a way to highlight individuals in the plot where there is a discrepancy between their prior (k-means) and posterior (DAPC membership probability) grouping?

I also was wondering if it's possible to assign different symbols to individuals according to their population or species (as defined in the input file) in the scatter plot. This seems to be possible as I found this Figure (see below) in a recent publication (Wofford AM, Finch K, Bigott A, Willyard A (2014) A Set of Plastid Loci for Use in Multiplex Fragment Length Genotyping for Intraspecific Variation in Pinus (Pinaceae). Applications in Plant Sciences)

[cid:image005.jpg at 01CF6AB6.7C916810]

This would be very useful because at the moment I can see that there are 3 groups in my plot (see below) but I don't know if these groups more or less correspond to my population definitions, for example are all the individuals in group 3 from one population or are there also samples from other pops? I am aware that I can check this with the table.value command but it would be a lot easier to see this info at a glance from the plot.

[cid:image006.jpg at 01CF6AB6.7C916810]

Thank you


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