cytoscape_graph#

cytoscape_graph(data, attrs=None, name='name', ident='id')[source]#

Create a NetworkX graph from a dictionary in cytoscape JSON format.

Parameters:

datadict: A dictionary of data conforming to cytoscape JSON format.
attrsdict or None (default=None): A dictionary containing the keys ‘name’ and ‘ident’ which are mapped to the ‘name’ and ‘id’ node elements in cyjs format. All other keys are ignored. Default is None which results in the default mapping dict(name="name", ident="id").

Deprecated since version 2.6: The attrs keyword argument will be replaced with name and ident in networkx 3.0
namestring: A string which is mapped to the ‘name’ node element in cyjs format. Must not have the same value as ident.
identstring: A string which is mapped to the ‘id’ node element in cyjs format. Must not have the same value as name.

Returns:

grapha NetworkX graph instance: The graph can be an instance of Graph, DiGraph, MultiGraph, or MultiDiGraph depending on the input data.

Raises:

NetworkXError: If the name and ident attributes are identical.

See also

cytoscape_data: convert a NetworkX graph to a dict in cyjs format

References

[1]

Cytoscape user’s manual: http://manual.cytoscape.org/en/stable/index.html

Examples

>>> data_dict = {
...     'data': [],
...     'directed': False,
...     'multigraph': False,
...     'elements': {'nodes': [{'data': {'id': '0', 'value': 0, 'name': '0'}},
...       {'data': {'id': '1', 'value': 1, 'name': '1'}}],
...      'edges': [{'data': {'source': 0, 'target': 1}}]}
... }
>>> G = nx.cytoscape_graph(data_dict)
>>> G.name
''
>>> G.nodes()
NodeView((0, 1))
>>> G.nodes(data=True)[0]
{'id': '0', 'value': 0, 'name': '0'}
>>> G.edges(data=True)
EdgeDataView([(0, 1, {'source': 0, 'target': 1})])