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]