Reference

• Module contents
  • main()
  • validate_percentage()
• Runner module
• PPI module
  • CosineSimilarityPPIGenerator
    • CosineSimilarityPPIGenerator.PPI_CUTOFFS
    • CosineSimilarityPPIGenerator.get_next_network()
  • PPINetworkGenerator
    • PPINetworkGenerator.get_next_network()
• Hierarchy module
  • CDAPSHiDeFHierarchyGenerator
    • CDAPSHiDeFHierarchyGenerator.ATTR_DEC_NAME
    • CDAPSHiDeFHierarchyGenerator.BOOTSTRAP_EDGES
    • CDAPSHiDeFHierarchyGenerator.CDAPS_JSON_FILE
    • CDAPSHiDeFHierarchyGenerator.CDRES_KEY_NAME
    • CDAPSHiDeFHierarchyGenerator.EDGELIST_TSV
    • CDAPSHiDeFHierarchyGenerator.HIDEF_OUT_PREFIX
    • CDAPSHiDeFHierarchyGenerator.HIERARCHY_PARENT_CUTOFF
    • CDAPSHiDeFHierarchyGenerator.NODE_CX_KEY_NAME
    • CDAPSHiDeFHierarchyGenerator.PERSISTENCE_COL_NAME
    • CDAPSHiDeFHierarchyGenerator.TRANSLATED_HIDEF_OUT_PREFIX
    • CDAPSHiDeFHierarchyGenerator.convert_hidef_output_to_cdaps()
    • CDAPSHiDeFHierarchyGenerator.get_hierarchy()
    • CDAPSHiDeFHierarchyGenerator.get_hierarchy_from_edgelists()
    • CDAPSHiDeFHierarchyGenerator.update_cluster_node_map()
    • CDAPSHiDeFHierarchyGenerator.update_persistence_map()
    • CDAPSHiDeFHierarchyGenerator.write_communities()
    • CDAPSHiDeFHierarchyGenerator.write_members_for_row()
    • CDAPSHiDeFHierarchyGenerator.write_persistence_node_attribute()
  • HierarchyGenerator
    • HierarchyGenerator.get_generated_dataset_ids()
    • HierarchyGenerator.get_hierarchy()
• Mature hierarchy module
  • HiDeFHierarchyRefiner
    • HiDeFHierarchyRefiner.CHILD_COL
    • HiDeFHierarchyRefiner.CONTAINMENT_THRESHOLD
    • HiDeFHierarchyRefiner.DEFAULT_TYPE
    • HiDeFHierarchyRefiner.EDGES_SUFFIX
    • HiDeFHierarchyRefiner.GENES_COL
    • HiDeFHierarchyRefiner.GENE_TYPE
    • HiDeFHierarchyRefiner.JACCARD_THRESHOLD
    • HiDeFHierarchyRefiner.MIN_DIFF
    • HiDeFHierarchyRefiner.MIN_SYSTEM_SIZE
    • HiDeFHierarchyRefiner.NODES_SUFFIX
    • HiDeFHierarchyRefiner.PARENT_COL
    • HiDeFHierarchyRefiner.STABILITY_COL
    • HiDeFHierarchyRefiner.TERMS_COL
    • HiDeFHierarchyRefiner.TSIZE_COL
    • HiDeFHierarchyRefiner.TYPE_COL
    • HiDeFHierarchyRefiner.refine_hierarchy()
• HCX (Hierarchy in CX2) module
  • HCXFromCDAPSCXHierarchy
    • HCXFromCDAPSCXHierarchy.VISUAL_EDITOR_PROPERTIES_ASPECT
    • HCXFromCDAPSCXHierarchy.apply_style_to_network()
    • HCXFromCDAPSCXHierarchy.get_converted_hierarchy()
• Layout module
  • CytoscapeJSBreadthFirstLayout
    • CytoscapeJSBreadthFirstLayout.HEADERS
    • CytoscapeJSBreadthFirstLayout.add_layout()
  • HierarchyLayout
    • HierarchyLayout.add_layout()
• NDEx Upload module
  • NDExHierarchyUploader
    • NDExHierarchyUploader.get_cytoscape_url()
    • NDExHierarchyUploader.save_hierarchy_and_parent_network()
    • NDExHierarchyUploader.upload_hierary_and_parent_network_from_files()
• Exceptions
  • CellmapsGenerateHierarchyError