I like this idea :+1: if we have a object to represent all of these coordinate types, then plotting all of these files should become way simpler!

On Feb 13, 2014, at 3:08 PM, Jai Ram Rideout <notifications@github.com> wrote:

> In bipy/maths/stats/ordination/base.py:
> 
> > +                                    ('eigvals', 'objects', 'descriptors',
> > +                                     'biplot', 'site_constraints'))):
> > +    __slots__ = ()
> > +
> > +    def __new__(cls, eigvals, objects, descriptors=None, biplot=None,
> > +                site_constraints=None):
> > +        return super(OrdinationResults2, cls).__new__(cls, eigvals, objects,
> > +                                                      descriptors, biplot,
> > +                                                      site_constraints)
> > +
> > +
> > +class Ordination(object):
> > +    short_method_name = 'Overwrite in subclass!'
> > +    long_method_name = 'Overwrite in subclass!'
> > +
> > +    def biplot(self, scaling=2, choices=[0, 1]):
> Cool, and I agree with @antgonza that we should coordinate (pun intended?) file formats and Python objects to store the results, so that visualization can be done in Emperor.
> 
> This is related to an open QIIME issue where NMDS coordinate files don't work with make_2d_plots.py, make_3d_plots.py, or Emperor:
> 
> qiime/qiime#1341
> 
> I think it's time for a Coordinates class in bipy. This class would be a data container with serialization methods, similar to DistanceMatrix. What do you guys think?
> 
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