[adegenet-forum] PCA and DAPC

[Roy Francis Mathew]

Hi,

I work with diploid microsatellite data. The PCA on this data works fine.

The different populations can be given different colours.

I was wondering if the different populations could be given different pch values. I tried to work this out, but doesn't work.

It would also be nice if some populations could be hidden for better clarity. 

I have sort of succeeded at this by giving colour value 0 for the populations that I want hidden, but its not the best idea.

 

I have tried to use plot3d from rgl package for PCA and it gives out 3d result, but I cannot color code different populations or pch differentiate pops.

 

Finally I was wondering if a tutorial was made on DAPC analysis and find.clusters/assign.plot etc.

I am currently using structure, but wish to move to DAPC on R.

 

 

Kind regards 

Roy Mathew Francis

Dept. of Integrated Pest Management
Faculty of Agricultural Sciences
Aarhus University
Forsøgsvej 1
DK-4200 Slagelse

 

Tel.: +45 
Email: RoyFrancis.Mathew at agrsci.dk


Tel.: +45 8999 1900
Web: www.agrsci.au.dk

 

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