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

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

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