Cytoscape networks (
This class assembles a CX network from a set of INDRA Statements.
The CX format is an aspect oriented data mode for networks. The format is defined at http://www.home.ndexbio.org/data-model/. The CX format is the standard for NDEx and is compatible with CytoScape via the CyNDEx plugin.
- stmts (Optional[list[indra.statements.Statement]]) – A list of INDRA Statements to be assembled.
- network_name (Optional[str]) – The name of the network to be assembled. Default: indra_assembled
list[indra.statements.Statement] – A list of INDRA Statements to be assembled.
str – The name of the network to be assembled.
dict – The structure of the CX network that is assembled.
Add INDRA Statements to the assembler’s list of statements.
Parameters: stmts (list[indra.statements.Statement]) – A list of
indra.statements.Statementto be added to the statement list of the assembler.
Assemble the CX network from the collected INDRA Statements.
This method assembles a CX network from the set of INDRA Statements. The assembled network is set as the assembler’s cx argument.
Parameters: add_indra_json (Optional[bool]) – If True, the INDRA Statement JSON annotation is added to each edge in the network. Default: True Returns: cx_str – The json serialized CX model. Return type: str
Return the assembled CX network as a json string.
Parameters: pretty (bool) – If True, the CX string is formatted with indentation (for human viewing) otherwise no indentation is used. Returns: json_str – A json formatted string representation of the CX network. Return type: str
Save the assembled CX network in a file.
Parameters: file_name (Optional[str]) – The name of the file to save the CX network to. Default: model.cx
Set protein expression data and mutational status as node attribute
This method uses
indra.databases.context_clientto get protein expression levels and mutational status for a given cell type and set a node attribute for proteins accordingly.
Parameters: cell_type (str) – Cell type name for which expression levels are queried. The cell type name follows the CCLE database conventions. Example: LOXIMVI_SKIN, BT20_BREAST
Creates a new NDEx network of the assembled CX model.
To upload the assembled CX model to NDEx, you need to have a registered account on NDEx (http://ndexbio.org/) and have the ndex python package installed. The uploaded network is private by default.
Parameters: ndex_cred (dict) – A dictionary with the following entries: ‘user’: NDEx user name ‘password’: NDEx password Returns: network_id – The UUID of the NDEx network that was created by uploading the assembled CX model. Return type: str