iggytop.io.create_knowledge_graph

iggytop.io.create_knowledge_graph#

Functions

create_knowledge_graph([cache_dir, ...])

Generates the knowledge graph using specified adapters and saves it in the requested format.
iggytop.io.create_knowledge_graph.create_knowledge_graph(cache_dir='/home/docs/.cache/iggytop', test_mode=False, receptors_to_include=['TCR', 'BCR'], adapters_to_include=['VDJDB', 'MCPAS', 'TRAIT', 'IEDB', 'TCR3D', 'NEOTCR', 'CEDAR', 'ITRAP'], output_format=None, filter_10x=False)#

Generates the knowledge graph using specified adapters and saves it in the requested format.

Parameters:

  • cache_dir (str, optional) – Directory to store cache and output files. Includes raw datasets and generated knowledge graphs (see logs for filenames). Defaults to user cache directory.

  • test_mode (bool, optional) – Test mode will use only 1% of the data for faster execution. Defaults to False.

  • receptors_to_include (List[str], optional) – List of receptor types to include in the knowledge graph. Available receptor types: [“TCR”, “BCR”]. Defaults to including both TCR and BCR.

  • adapters_to_include (List[str], optional) – List of adapter names to run. Available adapters: [“VDJDB”, “MCPAS”, “TRAIT”, “IEDB”, “TCR3D”, “NEOTCR”, “CEDAR”, “ITRAP”]. Defaults to providing all available adapters.

  • output_format (str, optional) – Output format, currently either ‘airr’,’neo4j’ or ‘networkx’

  • filter_10x (bool, optional) – Whether to filter out 10X Genomics datasets. Defaults to False.

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