def cancers(site_type):
result = pan_cancer_analysis(site_type)
counts = counts_by('cancer_type', result['all_active_mutations'])
cancer_by_code = {cancer.code: cancer.name for cancer in Cancer.query}
return (counts.keys(), counts.values(), [
f'{cancer_by_code[cancer_type]}: {count} mutations'
for cancer_type, count in counts.items()
])
def cancers_ontology(site_type, significant=True, vector=False):
result = pan_cancer_analysis(site_type)
cancer_by_code = {cancer.code: cancer.name for cancer in Cancer.query}
mutations = cancer_mutations(result, significant=significant)
terms = counts_by('cancer_name', mutations)
return ontology_plots(terms,
'cancers',
vector, [0, 70, 75, 80, 85, 90, 95],
allow_misses=False,
limit_to=['diseases', 'mondo'])
def merged_cancer_mutations(site_type):
all_cancer_mutations = [cancer_mutations(pan_cancer_analysis(site_type))]
ad_per_cancer = per_cancer_analysis(site_type)
for cancer_type, result in ad_per_cancer.items():
mutations = cancer_mutations(result, cancer_type=cancer_type)
all_cancer_mutations.append(mutations)
def pan_cancer_active_driver_with_bg(site_type):
result = pan_cancer_analysis(site_type.name)
return active_driver_gene_ontology(result['profile_against_genes_with_sites'])
def pan_cancer_active_driver(site_type):
result = pan_cancer_analysis(site_type.name)
return active_driver_gene_ontology(result['profile'])