def to_printable_graph(self, enrichment, graph):
viz_graph = DiGraph()
viz_graph.attrs["defaultnodesize"] = "labelsize"
viz_graph.attrs["label"] = str(enrichment)
entry_labels = {}
for entry in enrichment.entries:
if entry.p_value < self.min_p:
self.min_p = entry.p_value
if entry.p_value > self.max_p:
self.max_p = entry.p_value
for entry in enrichment.entries:
new_label = self.entry_to_label(entry)
viz_graph.add_node(new_label, self.to_printable_data(entry))
entry_labels[entry.id] = new_label
for label, node in graph.nodes.items():
if label not in entry_labels:
new_label = self.term_to_label(node.data)
viz_graph.add_node(new_label,
self.term_to_printable(node.data))
entry_labels[label] = new_label
for label, u in graph.nodes.items():
for edge in u.succ:
viz_graph.add_edge(entry_labels[label],
entry_labels[edge.to_node.label])
return viz_graph
def to_printable_graph(self, enrichment, graph):
viz_graph = DiGraph()
viz_graph.attrs["defaultnodesize"] = "labelsize"
viz_graph.attrs["label"] = str(enrichment)
entry_labels = {}
for entry in enrichment.entries:
if entry.p_value < self.min_p:
self.min_p = entry.p_value
if entry.p_value > self.max_p:
self.max_p = entry.p_value
for entry in enrichment.entries:
new_label = self.entry_to_label(entry)
viz_graph.add_node(new_label, self.to_printable_data(entry))
entry_labels[entry.id] = new_label
for label, node in graph.nodes.items():
if label not in entry_labels:
new_label = self.term_to_label(node.data)
viz_graph.add_node(new_label, self.term_to_printable(node.data))
entry_labels[label] = new_label
for label, u in graph.nodes.items():
for edge in u.succ:
viz_graph.add_edge(entry_labels[label], entry_labels[edge.to_node.label])
return viz_graph
def test_write(self):
correct_output_a = """graph [
directed 1
node [
id 0
label "1"
a 1
]
node [
id 1
label "2"
]
edge [
source 0
target 1
x "x"
]
edge [
source 1
target 0
label "zzzz"
]
]"""
correct_output_b = """graph [
directed 1
node [
id 0
label "2"
]
node [
id 1
label "1"
a 1
]
edge [
source 1
target 0
x "x"
]
edge [
source 0
target 1
label "zzzz"
]
]"""
out = StringIO()
writer = GmlWriter(out)
graph = DiGraph()
graph.add_node(1, {'a': 1})
graph.add_edge(1, 2, {'x': 'x'})
graph.add_edge(2, 1, "zzzz")
writer.write(graph)
self.assertIn(out.getvalue(), set([correct_output_a,
correct_output_b]))
def test_write(self):
correct_output_a = """graph [
directed 1
node [
id 0
label "1"
a 1
]
node [
id 1
label "2"
]
edge [
source 0
target 1
x "x"
]
edge [
source 1
target 0
label "zzzz"
]
]"""
correct_output_b = """graph [
directed 1
node [
id 0
label "2"
]
node [
id 1
label "1"
a 1
]
edge [
source 1
target 0
x "x"
]
edge [
source 0
target 1
label "zzzz"
]
]"""
out = StringIO()
writer = GmlWriter(out)
graph = DiGraph()
graph.add_node(1, {'a' : 1 })
graph.add_edge(1, 2, {'x' : 'x'})
graph.add_edge(2, 1, "zzzz")
writer.write(graph)
self.assertIn(out.getvalue(), set([correct_output_a, correct_output_b]))
def test__get_reachable(self):
g = DiGraph([(1,2), (2,3), (3,4), (3,5), (5,2), (5,6), (6,8), (6,7), (2,9), (9,2)])
reachable_from_2 = g._get_reachable(g.get_node(2))
expected = ([], set([2, 3, 4, 5, 6, 7, 8, 9]))
self.assertEqual(expected, reachable_from_2)
reachable_from_6 = g._get_reachable(g.get_node(6))
expected = ([], set([8, 7]))
self.assertEqual(expected, reachable_from_6)
# Found cycles
expected = [[2, 9], [2, 5, 3]]
self.assertEqual(expected, g.cycles)
def __init__(self):
DiGraph.__init__(self)
self.typedefs = {}
self.synonyms = {}
def __init__(self):
DiGraph.__init__(self)
self.typedefs = {}
self.synonyms = {}
def test_write(self):
correct_output = """graph [
directed 1
node [
id 0
label "1"
a 1
abb "[1, 2]"
bb 2
]
node [
id 1
label "2"
]
node [
id 2
label "3"
]
node [
id 3
label "4"
]
node [
id 4
label "5"
]
edge [
source 0
target 1
]
edge [
source 0
target 3
x "x"
]
edge [
source 1
target 2
]
edge [
source 2
target 3
]
edge [
source 2
target 4
]
edge [
source 4
target 1
label "zzzz"
]
]"""
out = StringIO()
writer = GmlWriter(out)
graph = DiGraph([(1,2), (2,3), (3,4), (3,5)])
graph.update_node(1, {'a' : 1, 'bb' : 2, 'abb' : [1, 2] })
graph.add_edge(1, 4, {'x' : 'x'})
graph.add_edge(5, 2, "zzzz")
writer.write(graph)
self.assertEqual(correct_output, out.getvalue())