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 visualise_tree(root=None, exact_order=True):
# tree = read_dendrogram_tree(PATH_DEND_JSON)
dend = nomenclature_2_nodes_n_edges(PATH_NMN_TABLE)
tree = generate_dendrogram_tree(dend)
if root is not None:
tree = dfs_tree(tree, root)
marker_expressions = read_marker_file(PATH_MARKERS)
add_label_metadata(tree)
node_colors, node_labels, node_sizes, pos = decorate_nodes(
marker_expressions, tree)
all_leafs = [
x for x in tree.nodes(data=True) if tree.out_degree(x[0]) == 0
]
position_leaf_nodes(all_leafs, exact_order, pos)
position_intermediate_nodes(all_leafs, pos, tree)
# nx.draw_networkx(tree, pos, node_color=color_map, with_labels=False, arrows=False)
nx.draw_networkx_nodes(tree,
pos,
node_color=node_colors,
node_size=node_sizes)
nx.draw_networkx_edges(tree,
pos,
arrows=True,
connectionstyle="arc3,rad=0.1")
text = nx.draw_networkx_labels(tree, pos, node_labels, font_size=7)
rotate_leaf_labels(text)
plt.show()
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 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))