py4cytoscape.networks.add_cy_edges

add_cy_edges(source_target_list, edge_type='interacts with', directed=False, network=None, base_url='http://127.0.0.1:1234/v1')[source]

Add one or more edges to a Cytoscape network by listing source and target node pairs.

Parameters

  • source_target_list (list or list of lists) – Source and target node pairs

  • edgeType (str) – The type of interaction. Default is ‘interacts with’.

  • directed (bool) – Indicates whether interactions are directed. Default is FALSE.

  • network (SUID or str or None) – Name or SUID of a network or view. Default is the “current” network active in Cytoscape.

  • base_url (str) – Ignore unless you need to specify a custom domain, port or version to connect to the CyREST API. Default is http://127.0.0.1:1234 and the latest version of the CyREST API supported by this version of py4cytoscape.

Returns

A list of dicts for each edge (SUID, source, target) added.

Return type

list of dicts

Raises

  • CyError – if network name or SUID doesn’t exist, or if a source or target can’t resolve to just one node.

  • requests.exceptions.RequestException – if can’t connect to Cytoscape or Cytoscape returns an error

Examples

>>> add_cy_edges(['YLR075W', 'YKL028W'])
[{'SUID': 2884, 'source': 1552, 'target': 1698}]
>>> add_cy_edges([['YKL028W', 'YJR066W'], ['YJR066W', 'YLR452C'], ['YGR046W', 'YLR452C']])
[{'SUID': 2886, 'source': 1698, 'target': 1645}, {'SUID': 2887, 'source': 1645, 'target': 1534} ...]

Note

To identify a node whose name contains a comma, use ‘\’ to escape the comma. For example, ‘node1, node\,2’ identifies ‘node1’ and ‘node,2’.