def set_ic_ontology_struct(ontology: Ontology, relations: List[str] = None):
logger.info(
"Setting information content values based on ontology structure")
roots = ontology.get_roots(relations=relations)
for root_id in roots:
if "num_subsumers" not in ontology.node(root_id) and (
"type" not in ontology.node(root_id)
or ontology.node_type(root_id) == "CLASS"):
_set_num_subsumers_in_subgraph(ontology=ontology,
root_id=root_id,
relations=relations)
for root_id in roots:
if "num_leaves" not in ontology.node(root_id) and (
"type" not in ontology.node(root_id)
or ontology.node_type(root_id) == "CLASS"):
_set_num_leaves_in_subgraph(ontology=ontology,
root_id=root_id,
relations=relations)
for root_id in roots:
if "depth" not in ontology.node(root_id) and (
"type" not in ontology.node(root_id)
or ontology.node_type(root_id) == "CLASS"):
set_all_depths_in_subgraph(ontology=ontology,
root_id=root_id,
relations=relations)
for root_id in roots:
if "type" not in ontology.node(root_id) or ontology.node_type(
root_id) == "CLASS":
_set_information_content_in_subgraph(
ontology=ontology,
root_id=root_id,
maxleaves=ontology.node(root_id)["num_leaves"],
relations=relations)
logger.info("Finished setting information content values")
def set_all_depths(ontology: Ontology,
relations: List[str] = None,
comparison_func=max):
for root_id in ontology.get_roots():
if "type" not in ontology.node(root_id) or ontology.node_type(
root_id) == "CLASS":
set_all_depths_in_subgraph(ontology=ontology,
root_id=root_id,
relations=relations,
comparison_func=comparison_func)
for node_id, node_content in ontology.nodes().items():
if "depth" not in node_content:
node_content["depth"] = 0
def set_ic_annot_freq(ontology: Ontology, annotations: AssociationSet):
logger.info(
"Setting information content values based on annotation frequency")
for node_id in ontology.nodes():
node_prop = ontology.node(node_id)
if "rel_annot_genes" in node_prop:
del node_prop["rel_annot_genes"]
if "tot_annot_genes" in node_prop:
del node_prop["tot_annot_genes"]
if "IC" in node_prop:
del node_prop["IC"]
for root_id in ontology.get_roots():
if "depth" not in ontology.node(root_id) and (
"type" not in ontology.node(root_id)
or ontology.node_type(root_id) == "CLASS"):
set_all_depths_in_subgraph(ontology=ontology, root_id=root_id)
node_gene_map = defaultdict(set)
for subj, obj in annotations.associations_by_subj_obj.keys():
node_gene_map[obj].add(subj)
for node_id in ontology.nodes():
node_pr = ontology.node(node_id)
node_pr["rel_annot_genes"] = node_gene_map[node_id]
for root_id in ontology.get_roots():
_set_tot_annots_in_subgraph(ontology, root_id)
for node_prop in ontology.nodes().values():
if "tot_annot_genes" not in node_prop:
node_prop["tot_annot_genes"] = set()
tot_annots = len(
set([
gene for set_genes in node_gene_map.values() for gene in set_genes
]))
min_annots = min([
len(node["tot_annot_genes"]) for node in ontology.nodes().values()
if "tot_annot_genes" in node and len(node["tot_annot_genes"]) > 0
])
if not min_annots:
min_annots = 1
for node_prop in ontology.nodes().values():
node_prop["IC"] = -math.log(len(node_prop["tot_annot_genes"]) / tot_annots) if \
len(node_prop["tot_annot_genes"]) > 0 else -math.log(min_annots / (tot_annots + 1))
logger.info("Finished setting information content values")