Index

A

add_layout() (cellmaps_generate_hierarchy.layout.CytoscapeJSBreadthFirstLayout method) (cellmaps_generate_hierarchy.layout.HierarchyLayout method)

apply_style_to_network() (cellmaps_generate_hierarchy.hcx.HCXFromCDAPSCXHierarchy static method) ATTR_DEC_NAME (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator attribute)

B

BOOTSTRAP_EDGES (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator attribute)

C

CDAPS_JSON_FILE (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator attribute) CDAPSHiDeFHierarchyGenerator (class in cellmaps_generate_hierarchy.hierarchy) CDRES_KEY_NAME (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator attribute) cellmaps_generate_hierarchy module cellmaps_generate_hierarchy.cellmaps_generate_hierarchycmd module cellmaps_generate_hierarchy.exceptions module cellmaps_generate_hierarchy.hcx module cellmaps_generate_hierarchy.hierarchy module

cellmaps_generate_hierarchy.layout module cellmaps_generate_hierarchy.maturehierarchy module cellmaps_generate_hierarchy.ndexupload module cellmaps_generate_hierarchy.ppi module CellmapsGenerateHierarchyError CHILD_COL (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner attribute) CONTAINMENT_THRESHOLD (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner attribute) convert_hidef_output_to_cdaps() (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator method) CosineSimilarityPPIGenerator (class in cellmaps_generate_hierarchy.ppi) CytoscapeJSBreadthFirstLayout (class in cellmaps_generate_hierarchy.layout)

D

DEFAULT_TYPE (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner attribute)

E

EDGELIST_TSV (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator attribute)

EDGES_SUFFIX (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner attribute)

G

GENE_TYPE (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner attribute) GENES_COL (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner attribute) get_converted_hierarchy() (cellmaps_generate_hierarchy.hcx.HCXFromCDAPSCXHierarchy method) get_cytoscape_url() (cellmaps_generate_hierarchy.ndexupload.NDExHierarchyUploader method) get_generated_dataset_ids() (cellmaps_generate_hierarchy.hierarchy.HierarchyGenerator method)

get_hierarchy() (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator method) (cellmaps_generate_hierarchy.hierarchy.HierarchyGenerator method) get_hierarchy_from_edgelists() (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator method) get_next_network() (cellmaps_generate_hierarchy.ppi.CosineSimilarityPPIGenerator method) (cellmaps_generate_hierarchy.ppi.PPINetworkGenerator method)

H

HCXFromCDAPSCXHierarchy (class in cellmaps_generate_hierarchy.hcx) HEADERS (cellmaps_generate_hierarchy.layout.CytoscapeJSBreadthFirstLayout attribute) HIDEF_OUT_PREFIX (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator attribute)

HiDeFHierarchyRefiner (class in cellmaps_generate_hierarchy.maturehierarchy) HIERARCHY_PARENT_CUTOFF (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator attribute) HierarchyGenerator (class in cellmaps_generate_hierarchy.hierarchy) HierarchyLayout (class in cellmaps_generate_hierarchy.layout)

J

JACCARD_THRESHOLD (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner attribute)

M

main() (in module cellmaps_generate_hierarchy.cellmaps_generate_hierarchycmd) MIN_DIFF (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner attribute) MIN_SYSTEM_SIZE (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner attribute) module cellmaps_generate_hierarchy cellmaps_generate_hierarchy.cellmaps_generate_hierarchycmd cellmaps_generate_hierarchy.exceptions cellmaps_generate_hierarchy.hcx cellmaps_generate_hierarchy.hierarchy cellmaps_generate_hierarchy.layout cellmaps_generate_hierarchy.maturehierarchy cellmaps_generate_hierarchy.ndexupload cellmaps_generate_hierarchy.ppi

N

NDExHierarchyUploader (class in cellmaps_generate_hierarchy.ndexupload)

NODE_CX_KEY_NAME (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator attribute) NODES_SUFFIX (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner attribute)

P

PARENT_COL (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner attribute) PERSISTENCE_COL_NAME (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator attribute)

PPI_CUTOFFS (cellmaps_generate_hierarchy.ppi.CosineSimilarityPPIGenerator attribute) PPINetworkGenerator (class in cellmaps_generate_hierarchy.ppi)

R

refine_hierarchy() (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner method)

S

save_hierarchy_and_parent_network() (cellmaps_generate_hierarchy.ndexupload.NDExHierarchyUploader method)

STABILITY_COL (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner attribute)

T

TERMS_COL (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner attribute) TRANSLATED_HIDEF_OUT_PREFIX (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator attribute)

TSIZE_COL (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner attribute) TYPE_COL (cellmaps_generate_hierarchy.maturehierarchy.HiDeFHierarchyRefiner attribute)

U

update_cluster_node_map() (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator method)

update_persistence_map() (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator method) upload_hierary_and_parent_network_from_files() (cellmaps_generate_hierarchy.ndexupload.NDExHierarchyUploader method)

V

validate_percentage() (in module cellmaps_generate_hierarchy.cellmaps_generate_hierarchycmd)

VISUAL_EDITOR_PROPERTIES_ASPECT (cellmaps_generate_hierarchy.hcx.HCXFromCDAPSCXHierarchy attribute)

W

write_communities() (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator method)

write_members_for_row() (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator method) write_persistence_node_attribute() (cellmaps_generate_hierarchy.hierarchy.CDAPSHiDeFHierarchyGenerator method)