py4cytoscape.groups.create_group

create_group(group_name, nodes=None, nodes_by_col='SUID', network=None, base_url='http://127.0.0.1:1234/v1')[source]

Create a group from the specified nodes.

Parameters

  • group_name (str) – The name used to identify and optionaly label the group

  • nodes (list or str or int or None) – List of nodes or keyword: selected, unselected or all. If node list: list of node names or SUIDs, comma-separated string of node names or SUIDs, or scalar node name or SUID). Node names should be found in the SUID column of the node table unless specified in nodes_by_col. If list is None, default is currently selected nodes.

  • nodes_by_col (str) – name of node table column corresponding to provided nodes list. Default is ‘SUID’.

  • network (SUID or str or None) – Name or SUID of a network. 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

{‘group’: SUID} where SUID identifies the node corresponding to the group

Return type

dict

Raises

  • CyError – if network name or SUID doesn’t exist

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

Examples

>>> create_group('Group 1', ['GDS1', 'SIP4', 'PDC1'], nodes_by_col='COMMON') # create group containing nodes by common name
{'group': 95335}
>>> create_group('Group 1', 'GDS1, SIP4, PDC1', nodes_by_col='COMMON') # create group containing nodes by common name
{'group': 95335}
>>> create_group('Group 1', [1344, 1502, 1723]) # create group containing nodes by node SUID
{'group': 95335}
>>> create_group('Group 1') # create group containing all selected nodes
{'group': 95335}
>>> create_group('Group 1', []) # create group with no nodes
{'group': 95335}
>>> create_group('Group 1', nodes='unselected') # create group with all unselected nodes
{'group': 95335}

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’.