def test_cellmesh_query_species(self):
print('mouse_results')
genes = ['HLA-DRB5',
'HLA-DQA1',
'HCG24',
'ARHGEF1',
'HLA-DPB1',
'SCN4A',
'TEAD2',
'HLA-DRB1',
'LST1',
'HLA-DQB1',
'AIM1L']
results = cellmesh.hypergeometric_test(genes, species='mouse')
print(results[0])
genes = ['MYH11',
'CNN1',
'ACTA2',
'MYL9',
'OPTC']
results = cellmesh.hypergeometric_test(genes, species='mouse')
print(results[0])
self.assertEqual(results[0][1], 'Myocytes, Smooth Muscle')
results = cellmesh.hypergeometric_test(genes, species='both')
print(results[0])
self.assertEqual(results[0][1], 'Myocytes, Smooth Muscle')
def test_cellmesh_query_basic(self):
genes = ['HLA-DRB5',
'HLA-DQA1',
'HCG24',
'ARHGEF1',
'HLA-DPB1',
'SCN4A',
'TEAD2',
'HLA-DRB1',
'LST1',
'HLA-DQB1',
'AIM1L']
results = cellmesh.hypergeometric_test(genes)
print(results[0])
self.assertEqual(results[0][1], 'Dendritic Cells')
genes = ['MYH11',
'CNN1',
'ACTA2',
'MYL9',
'OPTC']
results = cellmesh.hypergeometric_test(genes)
print(results[0])
self.assertEqual(results[0][1], 'Myocytes, Smooth Muscle')
def test_anatomy_query(self):
genes = ['Tnnt2',
'Ifit1',
'Ifit3',
'Ifit3b',
'Rsad2',
'Psd',
'Tbx20',
'Gata4',
'Iigp1',
'Lum',
'Cd34',
'Corin',
'Pgam2',
'Dcn']
results = cellmesh.hypergeometric_test(genes, db_dir=cellmesh.ANATOMY_DB_DIR)
print(results[0])
if query_method == 'cellmarker':
results = cellmarker.hypergeometric_test(
top_genes, species=species)
top_cells = [x[0] for x in results]
elif query_method == 'cellmarker_prob':
results = cellmarker_prob_method.prob_test(
top_genes, species=species)
top_cells = [x[0] for x in results]
elif query_method == 'panglao':
results = cellmarker.hypergeometric_test(
top_genes,
species=species,
db_dir=cellmarker.PANGLAO_DB_DIR)
top_cells = [x[0] for x in results]
elif query_method == 'cellmesh':
results = cellmesh.hypergeometric_test(top_genes,
species=species)
top_cells = [x[1] for x in results]
elif query_method == 'cellmesh_tfidf':
results = cellmesh.normed_hypergeometric_test(
top_genes, species=species)
top_cells = [x[1] for x in results]
elif query_method == 'aggregate':
results = query_aggregation.cellmarker_cellmesh_hypergeometric_test(
top_genes)
top_cells = [x[1] for x in results[1:]]
results = results[1:]
elif query_method == 'aggregate_2':
results = query_aggregation.cellmarker_cellmesh_tfidf_hypergeometric_test(
top_genes)
top_cells = [x[1] for x in results[1:]]
results = results[1:]