The code here is plotting things via matplotlib, is there a specific reason why this is the case? i. e. take advantage of some specific feature matplotlib has, it is needed like this for a publication, etc. If there is no specific reason then I would say let's try to make the plotting from Emperor only. Any ideas @Jorge-C and @antgonza?

As a side note the current code in charge of computing the needed data for the biplots is a port from what's in `qiime/biplots.py` so it would be great if we could take advantage of this new code.