navis.interfaces.r.init_rcatmaid¶
- navis.interfaces.r.init_rcatmaid(**kwargs)[source]¶
Initialize the R Catmaid package.
R package by Greg Jefferis: https://github.com/jefferis/rcatmaid
- Parameters:
remote_instance (CATMAID instance) – From pymaid.CatmaidInstance(). This is used to extract credentials. Overrides other credentials provided!
server (str, optional) – Use this to set server URL if no remote_instance is provided
http_user (str, optional) – Use this to set http user if no remote_instance is provided
http_password (str, optional) – Use this to set http password if no remote_instance is provided
api_token (str, optional) – Use this to set user token if no remote_instance is provided
- Returns:
catmaid – R object representing the rcatmaid library
- Return type:
R library
Examples
>>> from navis.interfaces import r >>> rcatmaid = r.init_rcatmaid(server='https://your.catmaid.server', ... authname='http_user', ... authpassword='http_pw', ... authtoken='Your token') >>> # You can now use rcatmaid functions. For example: >>> neuron = rcatmaid.read_neurons_catmaid(16) >>> neuron R object with classes: ('neuronlist', 'list') mapped to: [ListSexpVector] 16: <class 'rpy2.rinterface.ListSexpVector'> <rpy2.rinterface.ListSexpVector object at 0x123d46708> [RTYPES.VECSXP]