def plot_summary_axes(graph, lax, rax):
"""Plots your graph summary statistics on the given axes.
After, you should run :func:`plt.tight_layout` and you must run :func:`plt.show` to view.
Shows:
1. Count of nodes, grouped by function type
2. Count of edges, grouped by relation type
:param pybel.BELGraph graph: A BEL graph
:param lax: An axis object from matplotlib
:param rax: An axis object from matplotlib
Example usage:
>>> import matplotlib.pyplot as plt
>>> from pybel import from_pickle
>>> from pybel_tools.summary import plot_summary_axes
>>> graph = from_pickle('~/dev/bms/aetionomy/parkinsons.gpickle')
>>> fig, axes = plt.subplots(1, 2, figsize=(10, 4))
>>> plot_summary_axes(graph, axes[0], axes[1])
>>> plt.tight_layout()
>>> plt.show()
"""
ntc = count_functions(graph)
etc = count_relations(graph)
df = pd.DataFrame.from_dict(dict(ntc), orient='index')
df_ec = pd.DataFrame.from_dict(dict(etc), orient='index')
df.sort_values(0, ascending=True).plot(kind='barh', logx=True, ax=lax)
lax.set_title('Number of nodes: {}'.format(graph.number_of_nodes()))
df_ec.sort_values(0, ascending=True).plot(kind='barh', logx=True, ax=rax)
rax.set_title('Number of edges: {}'.format(graph.number_of_edges()))
def test_functions_egf(self):
"""Test counting nodes and grouping by function on the EGF graph."""
result = {
PROTEIN: 10,
COMPLEX: 1,
BIOPROCESS: 1,
}
self.assertEqual(set(result), get_functions(egf_graph))
self.assertEqual(result, count_functions(egf_graph))
def test_functions_sialic(self):
"""Test counting nodes and grouping by function on the sialic acid graph."""
result = {
PROTEIN: 7,
COMPLEX: 1,
ABUNDANCE: 1,
}
self.assertEqual(set(result), get_functions(sialic_acid_graph))
self.assertEqual(Counter(result), count_functions(sialic_acid_graph))
def test_functions_egf(self):
result = {PROTEIN: 10, COMPLEX: 1, BIOPROCESS: 1}
self.assertEqual(set(result), get_functions(egf_graph))
self.assertEqual(result, count_functions(egf_graph))
def test_functions_sialic(self):
result = {PROTEIN: 7, COMPLEX: 1, ABUNDANCE: 1}
self.assertEqual(set(result), get_functions(sialic_acid_graph))
self.assertEqual(result, count_functions(sialic_acid_graph))
def test_bel_nodes(self):
"""Test transforming kgml into bel nodes."""
notch_summary_flatten_nodes = count_functions(self.notch_bel_flatten)
notch_summary_unflatten_edges = count_relations(
self.notch_bel_unflatten)
notch_summary_unflatten_nodes = count_functions(
self.notch_bel_unflatten)
glycolysis_summary_unflatten_nodes = count_functions(
self.glycolysis_bel_unflatten)
glycolysis_summary_flatten_nodes = count_functions(
self.glycolysis_bel_flatten)
ppar_bel_unflatten_nodes = count_functions(self.ppar_bel_unflatten)
ppar_bel_unflatten_edges = count_relations(self.ppar_bel_unflatten)
ppar_bel_flatten_nodes = count_functions(self.ppar_bel_flatten)
ppar_bel_flatten_edges = count_relations(self.ppar_bel_flatten)
self.assertEqual(notch_summary_unflatten_nodes['Protein'], 48)
self.assertEqual(notch_summary_unflatten_nodes['Composite'], 15)
self.assertEqual(notch_summary_unflatten_nodes['Complex'], 4)
self.assertEqual(notch_summary_unflatten_nodes['BiologicalProcess'], 2)
self.assertEqual(notch_summary_unflatten_edges['decreases'], 6)
self.assertEqual(notch_summary_unflatten_edges['increases'], 9)
self.assertEqual(notch_summary_unflatten_edges['association'], 1)
self.assertEqual(notch_summary_flatten_nodes['Protein'], 48)
self.assertEqual(notch_summary_flatten_nodes['Composite'], 0)
self.assertEqual(notch_summary_flatten_nodes['Complex'], 4)
self.assertEqual(notch_summary_flatten_nodes['BiologicalProcess'], 2)
self.assertEqual(glycolysis_summary_flatten_nodes['Protein'], 68)
self.assertEqual(glycolysis_summary_flatten_nodes['Composite'], 0)
self.assertEqual(glycolysis_summary_flatten_nodes['Complex'], 0)
self.assertEqual(glycolysis_summary_flatten_nodes['Abundance'], 31)
self.assertEqual(glycolysis_summary_flatten_nodes['BiologicalProcess'],
7)
self.assertEqual(glycolysis_summary_unflatten_nodes['Protein'], 68)
self.assertEqual(glycolysis_summary_unflatten_nodes['Composite'], 18)
self.assertEqual(glycolysis_summary_unflatten_nodes['Complex'], 0)
self.assertEqual(glycolysis_summary_flatten_nodes['Abundance'], 31)
self.assertEqual(
glycolysis_summary_unflatten_nodes['BiologicalProcess'], 7)
self.assertEqual(
self.ppar_bel_unflatten.summary_dict()['Number of Nodes'], 5)
self.assertEqual(ppar_bel_unflatten_nodes['Abundance'], 2)
self.assertEqual(ppar_bel_unflatten_nodes['Composite'], 1)
# 1 protein BEL node and 1 phosphorylated protein BEL node
self.assertEqual(ppar_bel_unflatten_nodes['Protein'], 2)
self.assertEqual(
self.ppar_bel_unflatten.summary_dict()['Number of Edges'], 5)
self.assertEqual(ppar_bel_unflatten_edges['increases'], 2)
self.assertEqual(ppar_bel_unflatten_edges['hasComponent'], 2)
self.assertEqual(ppar_bel_unflatten_edges['hasVariant'], 1)
self.assertEqual(
self.ppar_bel_flatten.summary_dict()['Number of Nodes'], 4)
self.assertEqual(ppar_bel_flatten_nodes['Abundance'], 2)
self.assertEqual(ppar_bel_flatten_nodes['Composite'], 0)
self.assertEqual(ppar_bel_flatten_nodes['Protein'], 2)
self.assertEqual(
self.ppar_bel_flatten.summary_dict()['Number of Edges'], 5)
self.assertEqual(ppar_bel_flatten_edges['increases'], 4)
self.assertEqual(ppar_bel_flatten_edges['hasVariant'], 1)
