py4cytoscape.network_selection.select_nodes

select_nodes(nodes, by_col='SUID', preserve_current_selection=True, network=None, base_url='http://127.0.0.1:1234/v1')[source]

Select nodes in the network by SUID, name or other column values.

Parameters

  • nodes (str or list or int or None) – List of nodes as 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.

  • by_col (str) – Node table column to lookup up provide node values. Default is ‘SUID’.

  • preserve_current_selection (bool) – Whether to maintain previously selected nodes.

  • 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

{‘nodes’: [node list], ‘edges’: [edge list]}

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

>>> select_nodes(None)
{}
>>> select_nodes(['RAP1'], by_col='COMMON')
{'nodes': [107514], 'edges': []}
>>> select_nodes('RAP1, HIS4', by_col='COMMON')
{'nodes': [107514, 107511], 'edges': []}
>>> select_nodes([107514, 107511])
{'nodes': [107514, 107511], 'edges': []}
>>> select_nodes(107514])
{'nodes': [107514], 'edges': []}

Note

In the return value, node list is the SUIDs of newly selected nodes and edge list is always empty – dict is {} if no nodes were selected