def test_subtree_restrictions(self):
tree = read_dendrogram_tree(PATH_DEND_JSON)
marker_expressions = read_marker_file(PATH_MARKERS)
# have marker
marker_extended_expressions = extend_expressions(
tree, marker_expressions, ["CS202002013_123"])
# assert same IDs
self.assertEqual(marker_expressions.keys(),
marker_extended_expressions.keys())
self.assertTrue(
"CS202002013_123" in marker_extended_expressions.keys())
expressions = marker_extended_expressions["CS202002013_123"][
EXPRESSIONS]
# root should not have expressions
self.assertEqual(0, len(expressions))
# markers on the root node should not be inherited
expressions = marker_extended_expressions["CS202002013_125"][
EXPRESSIONS]
# only self expressions
self.assertTrue("ensembl:ENSMUSG00000029819" in expressions)
self.assertTrue("ensembl:ENSMUSG00000075270" in expressions)
self.assertEqual(2, len(expressions))
expressions = marker_extended_expressions["CS202002013_8"][EXPRESSIONS]
# self expressions
self.assertTrue("ensembl:ENSMUSG00000110002" in expressions)
self.assertTrue("ensembl:ENSMUSG00000029361" in expressions)
# inherited from 125
self.assertTrue("ensembl:ENSMUSG00000029819" in expressions)
self.assertTrue("ensembl:ENSMUSG00000075270" in expressions)
self.assertEqual(4, len(expressions))
def test_marker_enrichment(self):
tree = read_dendrogram_tree(PATH_DEND_JSON)
marker_expressions = read_marker_file(PATH_MARKERS)
marker_extended_expressions = extend_expressions(
tree, marker_expressions)
# assert same IDs
self.assertEqual(marker_expressions.keys(),
marker_extended_expressions.keys())
self.assertTrue("CS202002013_86" in marker_extended_expressions.keys())
expressions = marker_extended_expressions["CS202002013_86"][
EXPRESSIONS]
# self expressions
self.assertTrue("ensembl:ENSMUSG00000039519" in expressions)
self.assertTrue("ensembl:ENSMUSG00000028031" in expressions)
self.assertTrue("ensembl:ENSMUSG00000045648" in expressions)
# enriched from _207
self.assertTrue("ensembl:ENSMUSG00000004151" in expressions)
self.assertTrue("ensembl:ENSMUSG00000047907" in expressions)
# enriched from _179
self.assertTrue("ensembl:ENSMUSG00000053025" in expressions)
self.assertTrue("ensembl:ENSMUSG00000032503" in expressions)
self.assertEqual(7, len(expressions))
def test_tree_ancestors(self):
tree = read_dendrogram_tree(PATH_DEND_JSON)
ancestors = nx.ancestors(tree, "CS202002013_213")
self.assertEqual(3, len(ancestors))
self.assertTrue("CS202002013_212" in ancestors)
self.assertTrue("CS202002013_118" in ancestors)
self.assertTrue("CS202002013_117" in ancestors)
def test_tree_descendants(self):
tree = read_dendrogram_tree(PATH_DEND_JSON)
descendants = nx.descendants(tree, "CS202002013_183")
self.assertEqual(4, len(descendants))
# direct leaf
self.assertTrue("CS202002013_60" in descendants)
# direct child
self.assertTrue("CS202002013_184" in descendants)
# child of 184
self.assertTrue("CS202002013_58" in descendants)
self.assertTrue("CS202002013_59" in descendants)
def test_subtree_restrictions_out_tree(self):
tree = read_dendrogram_tree(PATH_DEND_JSON)
marker_expressions = read_marker_file(PATH_MARKERS)
# have marker
marker_extended_expressions = extend_expressions(
tree, marker_expressions, ["CS202002013_123"])
# assert same IDs
self.assertEqual(marker_expressions.keys(),
marker_extended_expressions.keys())
# out of subtree should not be enriched
expressions = marker_extended_expressions["CS202002013_207"][
EXPRESSIONS]
# only self expressions
self.assertTrue("ensembl:ENSMUSG00000004151" in expressions)
self.assertTrue("ensembl:ENSMUSG00000047907" in expressions)
self.assertEqual(2, len(expressions))
def test_subtree_restrictions2(self):
tree = read_dendrogram_tree(PATH_DEND_JSON)
marker_expressions = read_marker_file(PATH_MARKERS)
# don't have marker
marker_extended_expressions = extend_expressions(
tree, marker_expressions, ["CS202002013_121"])
# assert same IDs
self.assertEqual(marker_expressions.keys(),
marker_extended_expressions.keys())
self.assertFalse(
"CS202002013_121" in marker_extended_expressions.keys())
expressions = marker_extended_expressions["CS202002013_123"][
EXPRESSIONS]
# only self expressions
self.assertTrue("ensembl:ENSMUSG00000070880" in expressions)
self.assertTrue("ensembl:ENSMUSG00000098326" in expressions)
self.assertEqual(2, len(expressions))
expressions = marker_extended_expressions["CS202002013_125"][
EXPRESSIONS]
# self expressions
self.assertTrue("ensembl:ENSMUSG00000029819" in expressions)
self.assertTrue("ensembl:ENSMUSG00000075270" in expressions)
# inherited from 123
self.assertTrue("ensembl:ENSMUSG00000070880" in expressions)
self.assertTrue("ensembl:ENSMUSG00000098326" in expressions)
self.assertEqual(4, len(expressions))
expressions = marker_extended_expressions["CS202002013_8"][EXPRESSIONS]
# self expressions
self.assertTrue("ensembl:ENSMUSG00000110002" in expressions)
self.assertTrue("ensembl:ENSMUSG00000029361" in expressions)
# inherited from 125
self.assertTrue("ensembl:ENSMUSG00000029819" in expressions)
self.assertTrue("ensembl:ENSMUSG00000075270" in expressions)
# inherited from 123
self.assertTrue("ensembl:ENSMUSG00000070880" in expressions)
self.assertTrue("ensembl:ENSMUSG00000098326" in expressions)
self.assertEqual(6, len(expressions))
def generate_pattern_table_denormalised_markers(dend_json_path, output_filepath):
path_parts = dend_json_path.split(os.path.sep)
taxon = path_parts[len(path_parts) - 1].split(".")[0]
taxonomy_config = read_taxonomy_config(taxon)
dend = dend_json_2_nodes_n_edges(dend_json_path)
dend_tree = read_dendrogram_tree(dend_json_path)
marker_path = MARKER_PATH.format(str(taxon).replace("CCN", ""))
gene_db_path = ENSEMBLE_PATH.format(str(taxonomy_config["Reference_gene_list"][0]).strip().lower())
if taxonomy_config:
subtrees = get_subtrees(dend_tree, taxonomy_config)
gene_names = read_gene_data(gene_db_path)
denorm_markers = get_denorm_markers(taxon, gene_names)
minimal_markers = read_markers(marker_path, gene_names)
dl = []
for o in dend['nodes']:
if o['cell_set_accession'] in set.union(*subtrees):
d = dict()
d['defined_class'] = ALLEN_DEND_ + o['cell_set_accession']
d['gross_cell_type'] = get_gross_cell_type(o['cell_set_accession'], subtrees, taxonomy_config)
d['taxon'] = taxonomy_config['Species'][0]
d['brain_region'] = taxonomy_config['Brain_region'][0]
if o['cell_set_accession'] in denorm_markers:
d['denorm_marker_list'] = denorm_markers[o['cell_set_accession']]
d['minimal_marker_list'] = minimal_markers[o['cell_set_accession']]
else:
d['denorm_marker_list'] = ''
d['minimal_marker_list'] = ''
dl.append(d)
robot_template = pd.DataFrame.from_records(dl)
robot_template.to_csv(output_filepath, sep="\t", index=False)
def test_subtree_restrictions3(self):
tree = read_dendrogram_tree(PATH_DEND_JSON)
marker_expressions = read_marker_file(PATH_MARKERS)
marker_extended_expressions = extend_expressions(
tree, marker_expressions, ["CS202002013_132", "CS202002013_179"])
# assert same IDs
self.assertEqual(marker_expressions.keys(),
marker_extended_expressions.keys())
self.assertTrue(
"CS202002013_179" in marker_extended_expressions.keys())
expressions = marker_extended_expressions["CS202002013_179"][
EXPRESSIONS]
self.assertEqual(0, len(expressions))
# 207 is child of 179
self.assertTrue(
"CS202002013_207" in marker_extended_expressions.keys())
expressions = marker_extended_expressions["CS202002013_207"][
EXPRESSIONS]
# self expressions
self.assertTrue("ensembl:ENSMUSG00000004151" in expressions)
self.assertTrue("ensembl:ENSMUSG00000047907" in expressions)
self.assertEqual(2, len(expressions))
# 88 is child of 207
self.assertTrue("CS202002013_88" in marker_extended_expressions.keys())
expressions = marker_extended_expressions["CS202002013_88"][
EXPRESSIONS]
# self expressions
self.assertTrue("ensembl:ENSMUSG00000026344" in expressions)
self.assertTrue("ensembl:ENSMUSG00000047907" in expressions)
# enriched from _207
self.assertTrue("ensembl:ENSMUSG00000004151" in expressions)
self.assertTrue("ensembl:ENSMUSG00000047907" in expressions)
# one duplicate
self.assertEqual(3, len(expressions))
# 86 is child of 207
self.assertTrue("CS202002013_86" in marker_extended_expressions.keys())
expressions = marker_extended_expressions["CS202002013_86"][
EXPRESSIONS]
# self expressions
self.assertTrue("ensembl:ENSMUSG00000039519" in expressions)
self.assertTrue("ensembl:ENSMUSG00000028031" in expressions)
self.assertTrue("ensembl:ENSMUSG00000045648" in expressions)
# enriched from _207
self.assertTrue("ensembl:ENSMUSG00000004151" in expressions)
self.assertTrue("ensembl:ENSMUSG00000047907" in expressions)
self.assertEqual(5, len(expressions))
self.assertFalse(
"CS202002013_132" in marker_extended_expressions.keys())
# 133 is child of 132
self.assertTrue(
"CS202002013_133" in marker_extended_expressions.keys())
expressions = marker_extended_expressions["CS202002013_133"][
EXPRESSIONS]
# self expressions
self.assertTrue("ensembl:ENSMUSG00000044288" in expressions)
self.assertTrue("ensembl:ENSMUSG00000058897" in expressions)
self.assertEqual(2, len(expressions))
# 9 is child of 133
self.assertTrue("CS202002013_9" in marker_extended_expressions.keys())
expressions = marker_extended_expressions["CS202002013_9"][EXPRESSIONS]
# self expressions
self.assertTrue("ensembl:ENSMUSG00000039385" in expressions)
self.assertTrue("ensembl:ENSMUSG00000058897" in expressions)
self.assertTrue("ensembl:ENSMUSG00000015766" in expressions)
# enriched from _132
self.assertTrue("ensembl:ENSMUSG00000044288" in expressions)
self.assertTrue("ensembl:ENSMUSG00000058897" in expressions)
# one duplicate
self.assertEqual(4, len(expressions))
# 11 is child of 132
self.assertTrue("CS202002013_11" in marker_extended_expressions.keys())
expressions = marker_extended_expressions["CS202002013_11"][
EXPRESSIONS]
# self expressions
self.assertTrue("ensembl:ENSMUSG00000063661" in expressions)
self.assertTrue("ensembl:ENSMUSG00000042045" in expressions)
self.assertTrue("ensembl:ENSMUSG00000027849" in expressions)
# enriched from _132
self.assertTrue("ensembl:ENSMUSG00000044288" in expressions)
self.assertTrue("ensembl:ENSMUSG00000058897" in expressions)
self.assertEqual(5, len(expressions))