joey711/phyloseq — pull request #364 by chuckpr (2014-06-25 16:09:44+00:00)
Title: use wascores from vegan to get species scores for biplot when ordination...

... class is 'pcoa'.

When ordination class is "pcoa" and ```plot_ordination``` type is "taxa" or "biplot" ```plot_ordination``` just returns the sites scores for the given "axes" because the Vegan ```scores``` function doesn't support the "pcoa" ordination object. The class of the ordination object can be tested for and subsequently the Vegan ```wascores``` function can be used to calculate weighted averages of taxa for given "axes" if the class is "pcoa". Works with the current ```plot_ordination``` arguments/interface.

This is a belated pull request based on a quick discussion we had at your ASM poster.