py4cytoscape.style_values.get_node_position

get_node_position(node_names=None, network=None, base_url='http://127.0.0.1:1234/v1')[source]

Retrieve the actual x,y position of specified nodes.

Parameters

  • node_names (str or list or int or None) – List of nodes or None. 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 name column of the node table. If list is None, default is all nodes.

  • 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

with index as node_names values and columns x and y containing coordinates

Return type

dataframe

Raises

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

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

Examples

>>> get_node_position()
                x                    y
YIL052C 2628.866343678256  1180.9601936051579
YDL215C 1723.7108261001308 2230.935871095392
YLR432W 1660.9524948013027 2387.6488532731264
...
>>> get_node_position(['YDR429C', 'YMR005W', 'YDR142C'])
                x                    y
YDR429C 2628.866343678256  1180.9601936051579
YMR005W 1723.7108261001308 2230.935871095392
YDR142C 1660.9524948013027 2387.6488532731264
>>> get_node_position([432646, 432647, 432644])
                x                    y
432646  2628.866343678256  1180.9601936051579
432647  1723.7108261001308 2230.935871095392
432644  1660.9524948013027 2387.6488532731264
>>> get_node_position(node_names='YER112W', network='galFiltered.sif')
                x                    y
YER112W  2151.8481399429043 2326.677814454767

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’.