py4cytoscape.tables.map_table_column

map_table_column(column, species, map_from, map_to, force_single=True, table='node', namespace='default', network=None, base_url='http://127.0.0.1:1234/v1')[source]

Map Table Column.

Perform identifier mapping using an existing column of supported identifiers to populate a new column with identifiers mapped to the originals.

Supported species: Human, Mouse, Rat, Frog, Zebrafish, Fruit fly, Mosquito, Worm, Arabidopsis thaliana, Yeast, E. coli, Tuberculosis. Supported identifier types (depending on species): Ensembl, Entrez Gene, Uniprot-TrEMBL, miRBase, UniGene, HGNC (symbols), MGI, RGD, SGD, ZFIN, FlyBase, WormBase, TAIR.

Parameters

  • column (str) – Name of column containing identifiers of type specified by map.from

  • species (str) – Common name for species associated with identifiers, e.g., Human. See details.

  • map_from (str) – Type of identifier found in specified column. See details.

  • map.to (str) – Type of identifier to populate in new column. See details.

  • force.single (bool) – Whether to return only first result in cases of one-to-many mappings; otherwise the new column will hold lists of identifiers. Default is TRUE.

  • table (str) – name of Cytoscape table to load data into, e.g., node, edge or network; default is “node”

  • namespace (str) – Namespace of table. Default is “default”.

  • 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

contains map_from and map_to columns.

Return type

dataframe

Warning

If map_to is not unique, it will be suffixed with an incrementing number in parentheses, e.g., if mapIdentifiers is repeated on the same network. However, the original map_to column will be returned regardless.

Raises

  • HTTPError – if table or namespace or table doesn’t exist in network

  • CyError – if network name or SUID doesn’t exist, or if mapping parameter is invalid

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

Examples

>>> map_table_column('name','Yeast','Ensembl','SGD')
          name        SGD
17920  YER145C S000000947
17921  YMR058W S000004662
17922  YJL190C S000003726
...