Cytoscape networks (
- class indra.assemblers.cx.assembler.CxAssembler(stmts=None, network_name=None)
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.
Add INDRA Statements to the assembler’s list of statements.
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.
Return the assembled CX network as a json string.
Save the assembled CX network in a file.
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.
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
- upload_model(ndex_cred=None, private=True, style='default')
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.
ndex_cred (Optional[dict]) – A dictionary with the following entries: ‘user’: NDEx user name ‘password’: NDEx password
private (Optional[bool]) – Whether or not the created network will be private on NDEX.
style (Optional[str]) – This optional parameter can either be (1) The UUID of an existing NDEx network whose style should be applied to the new network. (2) Unspecified or ‘default’ to use the default INDRA-assembled network style. (3) None to not set a network style.
network_id – The UUID of the NDEx network that was created by uploading the assembled CX model.
- Return type
- class indra.assemblers.cx.assembler.NiceCxAssembler(stmts=None, network_name=None)
Assembles a Nice CX network from a set of INDRA Statements.
A Nice CX network object that is assembled from Statements.
- add_edge(a1_id, a2_id, stmt)
Add a Statement to the network as an edge.
Add an Agent to the network as a node.
- make_model(self_loops=False, network_attributes=None)
Return a Nice CX network object after running assembly.
The assembled Nice CX network.
- Return type
Return the CX string of the assembled model.