jaxley.modules.base.to_graph

to_graph(module, synapses=False, channels=False)

Export a jx.Module as a networkX compartment graph.

Constructs a nx.DiGraph from the module. Each compartment in the module is represented by a node in the graph. The edges between the nodes represent the connections between the compartments. These edges can either be connections between compartments within the same branch, between different branches or even between different cells. In the latter case the synapse parameters are stored as edge attributes. Only function allows one synapse per edge! Additionally, global attributes of the module, for example ncomp, are stored as graph attributes.

Exported graphs can be imported again to jaxley using the from_graph method.

Parameters:

• module (jx.Module) – A jaxley module or view instance.

• synapses (bool) – Whether to export synapses to the graph.

• channels (bool) – Whether to export ion channels to the graph.

Returns:

A networkx compartment. Has the same structure as a graph built with build_compartment_graph().

Return type:

nx.DiGraph

Example usage

cell = jx.read_swc("path_to_swc.swc", ncomp=1)
comp_graph = to_graph(cell)