cellmaps_ppi_embedding package
Submodules
cellmaps_ppi_embedding.cellmaps_ppi_embeddingcmd module
- cellmaps_ppi_embedding.cellmaps_ppi_embeddingcmd.main(args)[source]
Main entry point for program
- Parameters:
args (list) – arguments passed to command line usually
sys.argv[1:]()
- Returns:
return value of
cellmaps_ppi_embedding.runner.CellMapsPPIEmbedder.run()
or2
if an exception is raised- Return type:
cellmaps_ppi_embedding.exceptions module
cellmaps_ppi_embedding.runner module
- class cellmaps_ppi_embedding.runner.CellMapsPPIEmbedder(outdir=None, embedding_generator=None, inputdir=None, skip_logging=True, name=None, organization_name=None, project_name=None, provenance_utils=<cellmaps_utils.provenance.ProvenanceUtil object>, input_data_dict=None, provenance=None)[source]
Bases:
object
Class to run algorithm
Constructor
- Parameters:
- PPI_EDGELIST_FILEKEY = 'edgelist'
- static get_apms_edgelist_file(input_dir=None, edgelist_filename='ppi_edgelist.tsv')[source]
- Parameters:
edgelist_filename
input_dir
- Returns:
- Returns:
- class cellmaps_ppi_embedding.runner.EmbeddingGenerator(dimensions=1024)[source]
Bases:
object
Base class for implementations that generate network embeddings
Constructor
- class cellmaps_ppi_embedding.runner.FakeEmbeddingGenerator(ppi_downloaddir, dimensions=1024)[source]
Bases:
EmbeddingGenerator
Fakes PPI embedding
Constructor
- Parameters:
dimensions (int) – Desired size of output embedding
- class cellmaps_ppi_embedding.runner.Node2VecEmbeddingGenerator(nx_network, p=2, q=1, dimensions=1024, walk_length=80, num_walks=80, workers=8)[source]
Bases:
EmbeddingGenerator
Constructor
Module contents
Top-level package for cellmaps_ppi_embedding.