hannes-brt/flowvb

Gating Flow Cytometry Data with Variational Bayes

flowvb's Issues

AttributeError: 'Options' object has no attribute 'copy'

Calling a FlowVBAnalysis-object directly or calling the get_labels or get_soft_labels methods produces:

/Users/oceanhug/virtualenv/FlowVB/lib/python2.6/site-packages/flowvb/core/flow_vb.pyc in   __repr__(self)
     81 
     82         # Add data dimensions to data dictionary

---> 83         opt = self.options.copy()
     84         opt.update({'num_obs': self.data.shape[0],
     85                     'num_features': self.data.shape[1]})

Simpler interface for initialization options

Currently, the user has to import one of the Initialiser-subclasses and call initialise_parameters with the data and number of clusters (which in addition he has to provide to args.num_comp_init). The user should only have to supply the name of the initialization method he wants to use and the Initialiser-object should be created for him. Also, it would be simpler to make initialise_parameters the constructor.

FlowVBAnalysis should provide default parameters

The Options class should provide a set of sensible defaults for the parameters such that the user doesn't have to provide all parameters.