def label_som_patient_genes(self, all_pw_map, patients):
"""Labels all patients with matching level of expression
Parameters
----------
all_pw_map: :obj:`list` of :obj:`networkx.classes.graph.Graph`
a dictionary of all pathways we are using
patients: :obj:`list`
list of patients with mutation mappings
"""
# check if we already stored all over/under expression pathway data if so restore them
if self.som_pathways_save_valid(all_pw_map):
return self.restore_som_pathways(all_pw_map)
num_pat = len(patients)
# if there are missing ones calculate all of them
log('Somatic mutation patient pathway labeling')
for ind, patient in enumerate(patients):
pid = patient['pat_id']
genes = patient['mutated_nodes'] # get uniprot gene ids from indices
genes = np.array([genes])
log(f'Checking patient for somatic mutation {ind + 1:4}/{num_pat} pid={pid}')
label_mapper.mark_label_on_pathways('som', pid, all_pw_map, genes, self.label)
self.save_som_pathways(all_pw_map)
return all_pw_map
def label_cnv_patient_genes(self, all_pw_map, patients, cnv_type):
"""Labels all patients with matching level of expression
Parameters
----------
all_pw_map: :obj:`list` of :obj:`networkx.classes.graph.Graph`
a dictionary of all pathways we are using
patients: :obj:`dict`
mapping of patients with mutation mappings
"""
# check if we already stored all over/under expression pathway data if so restore them
if self.cnv_pathways_save_valid(all_pw_map, cnv_type):
return self.restore_cnv_pathways(all_pw_map, cnv_type)
num_pat = len(patients)
# if there are missing ones calculate all of them
log(f'CNV {cnv_type} patient pathway labeling')
ind = 1
for pid, patient in patients.items():
genes = np.array([patient[cnv_type]
]) # get uniprot gene ids from indices
logr(
f'Checking patient for cnv {cnv_type} {ind:4}/{num_pat} pid={pid}'
)
label_mapper.mark_label_on_pathways(f'cnv_{cnv_type}', pid,
all_pw_map, genes, self.label)
ind += 1
log()
self.save_cnv_pathways(all_pw_map, cnv_type)
return all_pw_map
def label_rppa_patient_genes(self, all_pw_map, pat_ids, GE, uni_ids):
"""Labels all patients with matching level of expression
Parameters
----------
all_pw_map: :obj:`list` of :obj:`networkx.classes.graph.Graph`
a dictionary of all pathways we are using
pat_ids: :obj:`list` of :obj:`str`
list of patient ids
GE: :obj:`numpy.ndarray`
Gene expression data array in shape of genes by patients
uni_ids: :obj:`numpy.ndarray`
mapping from uniprot to gene
"""
# check if we already stored all over/under expression pathway data if so restore them
if self.rppa_pathways_save_valid(all_pw_map):
return self.restore_rppa_pathways(all_pw_map)
num_pat = pat_ids.shape[0]
# if there are missing ones calculate all of them
log('RPPA Over and under expressed patient pathway labeling')
for ind, pid in enumerate(pat_ids):
if self.args.continuous:
gene_vals = (GE[..., pat_ids == pid]).flatten() # over expressed genes
logr(f'RPPA Checking patient for over-expressed {ind + 1:4}/{num_pat} pid={pid}')
label_mapper.mark_cont_label_on_pathways('oe', pid, all_pw_map, uni_ids, gene_vals)
label_mapper.mark_extra_label_on_pathways(f'oe-{self.label}', pid, all_pw_map, 'oe', self.threshold)
logr(f'RPPA Checking patient for under-expressed {ind + 1:4}/{num_pat} pid={pid}')
label_mapper.mark_cont_label_on_pathways('ue', pid, all_pw_map, uni_ids, gene_vals)
label_mapper.mark_extra_label_on_pathways(f'ue-{self.label}', pid, all_pw_map, 'ue', self.threshold)
else:
logr(f'RPPA Checking patient for rppa over-expressed {ind + 1:4}/{num_pat} pid={pid}')
gene_ind = (GE[..., pat_ids == pid] == 1).flatten() # over expressed genes
genes = uni_ids[gene_ind] # get uniprot gene ids from indices
label_mapper.mark_label_on_pathways('oe', pid, all_pw_map, genes, self.label)
logr(f'RPPA Checking patient for rppa under-expressed {ind + 1:4}/{num_pat} pid={pid}')
gene_ind = (GE[..., pat_ids == pid] == -1).flatten() # under expressed genes
genes = uni_ids[gene_ind] # get uniprot gene ids from indices
label_mapper.mark_label_on_pathways('ue', pid, all_pw_map, genes, self.label)
log()
self.save_rppa_pathways(all_pw_map)
return all_pw_map
def label_patient_genes(self, all_pw_map, pat_ids, ge, uni_ids):
"""Labels all patients with matching level of expression
Parameters
----------
all_pw_map: :obj:`list` of :obj:`networkx.classes.graph.Graph`
a dictionary of all pathways we are using
pat_ids: :obj:`list` of :obj:`str`
list of patient ids
ge: :obj:`numpy.ndarray`
Gene expression data array in shape of genes by patients
uni_ids: :obj:`numpy.ndarray`
Uniprot gene id mapping
"""
# check if we already stored all over/under expression pathway data if so restore them
if self.pathways_save_valid(all_pw_map):
return self.restore_pathways(all_pw_map)
num_pat = pat_ids.shape[0]
# if there are missing ones calculate all of them
log('Over and under expressed patient pathway labeling')
for ind, pid in enumerate(pat_ids):
log(f'Checking patient for over-expressed {ind + 1:4}/{num_pat} pid={pid}'
)
gene_ind = (
ge[..., pat_ids == pid] == 1).flatten() # over expressed genes
genes = uni_ids[gene_ind] # get uniprot gene ids from indices
label_mapper.mark_label_on_pathways('oe', pid, all_pw_map, genes,
self.label)
log(f'Checking patient for under-expressed {ind + 1:4}/{num_pat} pid={pid}'
)
gene_ind = (
ge[...,
pat_ids == pid] == -1).flatten() # under expressed genes
genes = uni_ids[gene_ind] # get uniprot gene ids from indices
label_mapper.mark_label_on_pathways('ue', pid, all_pw_map, genes,
self.label)
self.save_pathways(all_pw_map)
return all_pw_map
