diff --git a/.gitignore b/.gitignore
index 08c4f711312d1bdffe147c4cc94c6f7482c2c6b0..aee6a28d3bf803f6b2a5b8d9f73a674e3d8f8a1b 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,6 +2,7 @@ data/
real_data/
art/
**/__pycache__/
+*.pyc
.pytest_cache/
.idea/
.snakemake/
diff --git a/deconvolution/d2graph/d2_graph.py b/deconvolution/d2graph/d2_graph.py
index 1ccd369ea25aa1bd4aff16842e2982a2ea4eaba2..0b73ce55c64e1f7f19cf46ca1423ca5a2910999b 100644
--- a/deconvolution/d2graph/d2_graph.py
+++ b/deconvolution/d2graph/d2_graph.py
@@ -62,7 +62,7 @@ class D2Graph(nx.Graph):
return self.subgraph(list(self.nodes()))
- def construct_from_barcodes(self, neighbor_threshold=0.25, verbose=True, clique_mode=None, threads=1):
+ def construct_from_barcodes(self, neighbor_threshold=0.25, min_size_clique=4, verbose=False, clique_mode=None, threads=1):
# Compute all the d-graphs
if verbose:
print("Computing the unit d-graphs..")
@@ -70,8 +70,8 @@ class D2Graph(nx.Graph):
if clique_mode == "louvain":
dg_factory = LouvainDGFactory(self.barcode_graph)
else:
- dg_factory = CliqueDGFactory(self.barcode_graph, debug=self.debug, debug_path=self.debug_path)
- self.d_graphs_per_node = dg_factory.generate_all_dgraphs(threads=threads, verbose=True)
+ dg_factory = CliqueDGFactory(self.barcode_graph, min_size_clique=min_size_clique, debug=self.debug, debug_path=self.debug_path)
+ self.d_graphs_per_node = dg_factory.generate_all_dgraphs(threads=threads, verbose=verbose)
if verbose:
counts = sum(len(x) for x in self.d_graphs_per_node.values())
print(f"\t {counts} computed d-graphs")
diff --git a/deconvolution/dgraph/AbstractDGFactory.py b/deconvolution/dgraph/AbstractDGFactory.py
index 4ac14d20e2c8716ae8575e0f7d33f49d4da4b95c..8bae0c04fd57035c62c0938d075eccc7414ddb8e 100644
--- a/deconvolution/dgraph/AbstractDGFactory.py
+++ b/deconvolution/dgraph/AbstractDGFactory.py
@@ -17,7 +17,7 @@ def process_node(factory, node):
sys.stdout.flush()
# udg generation
- neighbors = list(factory.graph.neighbors(node))
+ neighbors = [x for x in factory.graph[node]]
subgraph = nx.Graph(factory.graph.subgraph(neighbors))
dgs = factory.generate_by_node(node, subgraph)
@@ -56,18 +56,25 @@ class AbstractDGFactory:
if verbose:
print("Start parallel work")
- results = None
- with Pool(processes=threads) as pool:
- results = pool.starmap(process_node, zip(
- [factory]*nb_nodes,
- self.graph.nodes()
- ))
-
- # Fill the index by node
- for node, dgs in results:
- key = frozenset({node})
- for dg in dgs:
- index.add_value(key, dg)
+ if threads > 1:
+ results = None
+ with Pool(processes=threads) as pool:
+ results = pool.starmap(process_node, zip(
+ [factory]*nb_nodes,
+ self.graph.nodes()
+ ))
+
+ # Fill the index by node
+ for node, dgs in results:
+ key = frozenset({node})
+ for dg in dgs:
+ index.add_value(key, dg)
+ else:
+ for node in self.graph.nodes():
+ key = frozenset({node})
+ _, dgs = process_node(factory, node)
+ for dg in dgs:
+ index.add_value(key, dg)
return index
@@ -75,5 +82,3 @@ class AbstractDGFactory:
@abstractmethod
def generate_by_node(self, node, subgraph):
pass
-
-
diff --git a/deconvolution/dgraph/CliqueDGFactory.py b/deconvolution/dgraph/CliqueDGFactory.py
index ce5acf5115cf19dc7b224cce51c4cf36cccb9e11..c30309bffbae53fa7c2f20384841a6f8a333f819 100644
--- a/deconvolution/dgraph/CliqueDGFactory.py
+++ b/deconvolution/dgraph/CliqueDGFactory.py
@@ -1,4 +1,5 @@
import networkx as nx
+from collections import Counter
from deconvolution.dgraph.AbstractDGFactory import AbstractDGFactory
from deconvolution.dgraph.d_graph import Dgraph
@@ -24,60 +25,86 @@ class CliqueDGFactory(AbstractDGFactory):
def generate_by_node(self, central_node, subgraph):
node_d_graphs = set()
+ node_neighbors = {node: [x for x in subgraph[node]] for node in subgraph.nodes}
# Clique computation
cliques = []
+ clique_neighbors_multiset = []
+ clique_neighbors_set = []
+ clq_per_node = {node: [] for node in subgraph.nodes}
+ idx = 0
for clique in nx.find_cliques(subgraph):
if len(clique) >= self.min_size:
- cliques.append(clique)
-
- # index cliques per node
- clq_per_node = {}
- for idx, clq in enumerate(cliques):
- for node in clq:
- if node not in clq_per_node:
- clq_per_node[node] = []
- clq_per_node[node].append(idx)
-
- # clq_per_node for nei can be empty because of minimum clique size
- for node in subgraph.nodes:
- if node not in clq_per_node:
- clq_per_node[node] = []
+ # Create the clique set
+ clique_set = frozenset(clique)
+ cliques.append(clique_set)
+
+ # Index neighbors of the clique to speedup the divergence computation
+ neighbors = []
+ for node in clique:
+ # index clique per node. Useful ?
+ clq_per_node[node].append(idx)
+ # Prepare a neighbor multiset to speedup the divergence computation
+ neighbors.extend(node_neighbors[node])
+ ms = Counter(neighbors)
+ clique_neighbors_multiset.append(ms)
+ clique_neighbors_set.append(frozenset(ms))
+ idx += 1
+
+ # def clique_divergence(c1, c2):
+ # # Observed link
+ # nb_links = 0
+ # for node in c1:
+ # neighbors = clique_neighbors[node]
+ #
+ # # Awaited links
+ # d_approx = max(len(c1), len(c2))
+ # awaited = d_approx * (d_approx - 1) / 2
+ #
+ # return abs(awaited - nb_links)
+
+ def clique_divergence(c1_idx, c1, c2):
+ observed_link = len(c1 & c2) # Intersections of the nodes are glued links
+ neighbor_intersection = clique_neighbors_set[c1_idx] & c2
+ neighbors_multiset = clique_neighbors_multiset[c1_idx]
+ observed_link += sum(neighbors_multiset[x] for x in neighbor_intersection) # Sum the links between the cliques
+
+ # Awaited links
+ d_approx = max(len(c1), len(c2))
+ awaited = d_approx * (d_approx - 1) / 2
+
+ return abs(awaited - observed_link)
# Pair cliques
- clq_pairs = set()
- for idx, clq in enumerate(cliques):
- for node in clq:
- neighbors = list(subgraph.neighbors(node))
- # Looks into the neighbors for clique pairing
- for nei in neighbors:
- nei_clqs = clq_per_node[nei]
- # Pair useful cliques
- for nei_clq in nei_clqs:
- if nei_clq > idx:
- clq_pairs.add((idx, nei_clq))
+ def enumerate_clique_pair():
+ for clq_idx, clq in enumerate(cliques):
+ for node in clq:
+ # Looks into the neighbors for clique pairing
+ for nei in subgraph[node]:
+ nei_clqs = clq_per_node[nei]
+ # Pair useful cliques
+ for nei_clq in nei_clqs:
+ if nei_clq > clq_idx:
+ div_clq = clique_divergence(clq_idx, clq, cliques[nei_clq])
+ yield clq_idx, nei_clq, div_clq
# Create the clique graph for max weight
clq_G = nx.Graph()
# Create nodes
for idx in range(len(cliques)):
clq_G.add_node(idx)
+
# Create edges
max_div = 0
- for idx1, idx2 in clq_pairs:
+ for idx1, idx2, div in enumerate_clique_pair():
# Get cliques
clq1 = cliques[idx1]
clq2 = cliques[idx2]
- # Create candidate udg
- d_graph = Dgraph(central_node)
- d_graph.put_halves(clq1, clq2, subgraph)
- # Add divergence to the clique graph
- div = d_graph.get_link_divergence()
if div > max_div:
max_div = div
clq_G.add_edge(idx1, idx2, weight=div)
# Normalize the divergence
- for idx1, idx2 in clq_pairs:
+ for idx1, idx2 in clq_G.edges():
clq_G.edges[idx1, idx2]['weight'] = max_div - clq_G.edges[idx1, idx2]['weight']
if self.debug and len(clq_G.nodes) > 0:
@@ -93,7 +120,7 @@ class CliqueDGFactory(AbstractDGFactory):
clq2 = cliques[idx2]
# Create candidate udg
d_graph = Dgraph(central_node)
- d_graph.put_halves(clq1, clq2, subgraph)
+ d_graph.put_halves(list(clq1), list(clq2), subgraph)
node_d_graphs.add(d_graph)
return node_d_graphs
diff --git a/experiments/clique_graph_eval.py b/experiments/clique_graph_eval.py
index 1dd9e5f5b4322ba0cd32a5dfff94f06f9d376dd7..f9697a1ceef6f60d7623ac1cf8f928b2401d5d3d 100644
--- a/experiments/clique_graph_eval.py
+++ b/experiments/clique_graph_eval.py
@@ -1,4 +1,5 @@
import argparse
+import time
import networkx as nx
from collections import Counter
@@ -79,7 +80,7 @@ def analyse_clique_graph(barcode_graph):
def analyse_d_graphs(barcode_graph):
# Generate udgs
factory = CliqueDGFactory(barcode_graph, 1)
- udg_per_node = factory.generate_all_dgraphs()
+ udg_per_node = factory.generate_all_dgraphs(threads=1)
# Remove duplicate udgs
udgs = {}
for udg_node_lst in udg_per_node.values():
@@ -99,14 +100,18 @@ def analyse_d_graphs(barcode_graph):
def main():
args = parse_arguments()
g = nx.read_gexf(args.barcode_graph)
+ prev_time = time.time()
continuous, total = analyse_clique_graph(g)
- print("cliques")
+ print("cliques", time.time() - prev_time)
print(continuous, "/", total)
+ prev_time = time.time()
continuous, total = analyse_d_graphs(g)
- print("udgs")
+ print("udgs", time.time() - prev_time)
print(continuous, "/", total)
if __name__ == "__main__":
+ # import cProfile
+ # cProfile.run('main()')
main()
diff --git a/setup.py b/setup.py
index 752551d18aa667f6b2d9cbbf12579284c5902f69..2f87c3bebae5dd4de1af0fee76682160e89131fc 100644
--- a/setup.py
+++ b/setup.py
@@ -4,7 +4,7 @@ from distutils.core import setup
setup(
name='10X-deconvolve',
version='0.1dev',
- packages=['deconvolution.d2graph', 'deconvolution.dgraph', 'deconvolution.main', 'experiments'],
+ packages=['deconvolution.d2graph', 'deconvolution.dgraph', 'deconvolution.main', 'experiments', 'tests'],
license='AGPL V3',
long_description=open('README.md').read(),
)
diff --git a/test_data/bar_1000_5_2.gexf b/test_data/bar_1000_5_2.gexf
new file mode 100644
index 0000000000000000000000000000000000000000..5dae7dcf1bd590f9dab4f9f84f2fa9f2ad7a9aab
--- /dev/null
+++ b/test_data/bar_1000_5_2.gexf
@@ -0,0 +1,5445 @@
+<?xml version='1.0' encoding='utf-8'?>
+<gexf version="1.2" xmlns="http://www.gexf.net/1.2draft" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.w3.org/2001/XMLSchema-instance">
+ <graph defaultedgetype="undirected" mode="static" name="">
+ <meta>
+ <creator>NetworkX 2.3</creator>
+ <lastmodified>31/01/2020</lastmodified>
+ </meta>
+ <nodes>
+ <node id="0:154_655" label="0:154_655" />
+ <node id="1:234_630" label="1:234_630" />
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diff --git a/tests/d2_graph_test.py b/tests/d2_graph_test.py
index 5d787431fe32abd67ada66f80b9c615c79e9c422..33dfb2f1c3e1e14e889540484352379b34f14ca5 100644
--- a/tests/d2_graph_test.py
+++ b/tests/d2_graph_test.py
@@ -8,84 +8,65 @@ from deconvolution.dgraph import graph_manipulator as gm
class TestD2Graph(unittest.TestCase):
- # def test_construction(self):
- # d2 = D2Graph(complete_graph)
- # d2.construct_from_barcodes(index_size=4, verbose=False)
+
+ # def test_linear_d2_construction(self):
+ # for d in range(2, 10):
+ # size = 2 * d + 3
+ #
+ # G = gm.generate_d_graph_chain(size, d)
+ # d2 = D2Graph(G)
+ # print("before", d)
+ # d2.construct_from_barcodes(neighbor_threshold=0, min_size_clique=d, verbose=False)
+ # print("after", d)
+ #
+ # # for dg in d2.all_d_graphs:
+ # # print(dg.score, dg.get_link_divergence(), dg)
+ # # print()
+ #
+ # # Test the number of d-graphs
+ # awaited_d_num = size - 2 * d
+ # self.assertEqual(awaited_d_num, len(d2.all_d_graphs))
#
- # # Evaluate the number of candidate unit d_graphs generated
- # for node, candidates in d2.d_graphs_per_node.items():
- # if node == "C" or node == "B2":
- # self.assertEqual(1, len(candidates))
- # else:
- # self.assertEqual(0, len(candidates))
+ # # Test connectivity
+ # # Center node names
+ # c1 = d
+ # c2 = d + 1
+ # c3 = d + 2
+ # # Connectivity matrix
+ # awaited_distances = {
+ # c1: {c2: 2, c3: 4},
+ # c2: {c1: 2, c3: 2},
+ # c3: {c1: 4, c2: 2}
+ # }
#
- # # Evaluate the dgraph
- # self.assertEqual(13, len(d2.index))
+ # for x, y, data in d2.edges(data=True):
+ # dg1 = d2.node_by_idx[x]
+ # dg2 = d2.node_by_idx[y]
#
- # overlap_key = ('A1', 'A2', 'B0', 'B1', 'B2', 'C')
- # for dmer, dg_lst in d2.index.items():
- # if dmer == overlap_key:
- # values = list(d2.index[dmer])
- # self.assertEqual(2, len(d2.index[dmer]))
- # self.assertNotEqual(values[0], values[1])
- # else:
- # self.assertEqual(1, len(d2.index[dmer]))
-
- def test_linear_d2_construction(self):
- for d in range(1, 10):
- size = 2 * d + 3
- index_k = 2 * d - 1
-
- G = gm.generate_d_graph_chain(size, d)
- d2 = D2Graph(G)
- d2.construct_from_barcodes(index_size=index_k, verbose=False)
-
-
- # for dg in d2.all_d_graphs:
- # print(dg.score, dg.get_link_divergence(), dg)
- # print()
-
- # Test the number of d-graphs
- awaited_d_num = size - 2 * d
- self.assertEqual(awaited_d_num, len(d2.all_d_graphs))
-
- # Test dgraph
- awaited_index_size = comb(2 * d + 1, index_k) + (size - (2 * d + 1)) * comb(2 * d, index_k - 1)
- if len(d2.index) != awaited_index_size:
- dmers = [list(x) for x in d2.index]
- dmers = [str(x) for x in dmers if len(x) != len(frozenset(x))]
-
- self.assertEqual(awaited_index_size, len(d2.index))
-
- # Test connectivity
- # Center node names
- c1 = d
- c2 = d + 1
- c3 = d + 2
- # Connectivity matrix
- awaited_distances = {
- c1: {c2: 2, c3: 4},
- c2: {c1: 2, c3: 2},
- c3: {c1: 4, c2: 2}
- }
-
- for x, y, data in d2.edges(data=True):
- dg1 = d2.node_by_idx[x]
- dg2 = d2.node_by_idx[y]
-
- awaited_dist = awaited_distances[dg1.center][dg2.center]
- self.assertEqual(data["distance"], awaited_dist)
+ # awaited_dist = awaited_distances[dg1.center][dg2.center]
+ # self.assertEqual(data["distance"], awaited_dist)
+
+ def test_no_variability(self):
+ barcode_graph = nx.read_gexf("test_data/bar_1000_5_2.gexf")
+ d2 = D2Graph(barcode_graph)
+ d2.construct_from_barcodes()
+ udgs = d2.all_d_graphs
+
+ for _ in range(5):
+ d2 = D2Graph(barcode_graph)
+ d2.construct_from_barcodes()
+ self.assertEqual(len(udgs), len(d2.all_d_graphs))
+
def test_reloading(self):
# Parameters
d = 3
size = 2 * d + 3
- index_k = 2 * d - 1
# Create a d2 graph
G = gm.generate_d_graph_chain(size, d)
d2 = D2Graph(G)
- d2.construct_from_barcodes(index_size=index_k, verbose=False)
+ d2.construct_from_barcodes(verbose=False)
# Save and reload the d2 in a temporary file
with tempfile.NamedTemporaryFile() as fp:
diff --git a/tests/d_graph_test.py b/tests/d_graph_test.py
index 16b746c3c90d8c12f0e4ede5e9dc2e0bb775fc82..e4b12e48dbf89f5a62e703f546089b288ba24a00 100644
--- a/tests/d_graph_test.py
+++ b/tests/d_graph_test.py
@@ -1,8 +1,10 @@
import unittest
+import networkx as nx
from d_graph_data import unit_d_graph
from deconvolution.dgraph.d_graph import Dgraph
from deconvolution.dgraph import graph_manipulator as gm
+from deconvolution.dgraph.CliqueDGFactory import CliqueDGFactory
class TestDGraph(unittest.TestCase):
@@ -60,9 +62,23 @@ class TestDGraph(unittest.TestCase):
self.assertEqual([['A0'], ['A1'], ['A2'], ['C'], ['B2'], ['B1'], ['B0']], lst)
-
- # def test_list_dgraphs(self):
-
+ def test_generation_no_variability_DGCliqueFactory(self):
+ barcode_graph = nx.read_gexf("test_data/bar_1000_5_2.gexf")
+ factory = CliqueDGFactory(barcode_graph, 1)
+ udg_per_node = factory.generate_all_dgraphs()
+ all_udgs = set()
+ for udgs in udg_per_node.values():
+ all_udgs.update(udgs)
+
+ size = len(all_udgs)
+ for _ in range(5):
+ factory = CliqueDGFactory(barcode_graph, 1)
+ udg_per_node = factory.generate_all_dgraphs()
+ all_udgs = set()
+ for udgs in udg_per_node.values():
+ all_udgs.update(udgs)
+
+ self.assertEqual(len(all_udgs), size)