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Friday, November 4, 2011

The major revision of MDLP: adding Yunusbayev et all.2011 data

Earlier this month i added Bulgarians, Ukrainians and Mordovians from the reference samples in Yunusbayev et all.2011 paper and calculated PCA loadings of new obtained

As promised earlier, i have wasted a couple of hours on plotting PCA loadings (from Eigensoft analysis of my MDL BGA project) in graphical interface of indispensable R-package "BiplotGUI". I've made a lot of efforts combining diffirent types of statistical tests into one meaningful illustration.

Below are results of my experiments with Biplot.

Another cool feature of BiplotGUI is that it fully supports rgl, which is a 3D visualization system based on OpenGL. It provides a medium to high level interface for use in R, currently modelled on classic R graphics, with extensions to allow for interaction and creation of 3D animations/movies.

I've not figured yet how it works, but the next time i will be doing PCA analysis, i'll try to make 3D rotating animations for members of my project. 

1 comment:

  1. It seems that you are wasting one dimension to components of a very small northern population using so many Finns. As a result the MDS-tool picks Saami components from Finnish samples and flattens the result of all other populations. Using more balanced population sizes you would get a more balanced plot. I consider the balance being distorted when the genetic source of some hundred tousands arctic people is the metric for whole Europe.