Python networkx.compose_all() Examples

def draw_stmt_graph(stmts):
    """Render the attributes of a list of Statements as directed graphs.

    The layout works well for a single Statement or a few Statements at a time.
    This function displays the plot of the graph using plt.show().

    Parameters
    ----------
    stmts : list[indra.statements.Statement]
        A list of one or more INDRA Statements whose attribute graph should
        be drawn.
    """
    import networkx
    try:
        import matplotlib.pyplot as plt
    except Exception:
        logger.error('Could not import matplotlib, not drawing graph.')
        return
    try:  # This checks whether networkx has this package to work with.
        import pygraphviz
    except Exception:
        logger.error('Could not import pygraphviz, not drawing graph.')
        return
    import numpy
    g = networkx.compose_all([stmt.to_graph() for stmt in stmts])
    plt.figure()
    plt.ion()
    g.graph['graph'] = {'rankdir': 'LR'}
    pos = networkx.drawing.nx_agraph.graphviz_layout(g, prog='dot')
    g = g.to_undirected()

    # Draw nodes
    options = {
        'marker': 'o',
        's': 200,
        'c': [0.85, 0.85, 1],
        'facecolor': '0.5',
        'lw': 0,
    }
    ax = plt.gca()
    nodelist = list(g)
    xy = numpy.asarray([pos[v] for v in nodelist])
    node_collection = ax.scatter(xy[:, 0], xy[:, 1], **options)
    node_collection.set_zorder(2)
    # Draw edges
    networkx.draw_networkx_edges(g, pos, arrows=False, edge_color='0.5')
    # Draw labels
    edge_labels = {(e[0], e[1]): e[2].get('label') for e in g.edges(data=True)}
    networkx.draw_networkx_edge_labels(g, pos, edge_labels=edge_labels)
    node_labels = {n[0]: n[1].get('label') for n in g.nodes(data=True)}
    for key, label in node_labels.items():
        if len(label) > 25:
            parts = label.split(' ')
            parts.insert(int(len(parts)/2), '\n')
            label = ' '.join(parts)
            node_labels[key] = label
    networkx.draw_networkx_labels(g, pos, labels=node_labels)
    ax.get_xaxis().set_visible(False)
    ax.get_yaxis().set_visible(False)
    plt.show() 

def simple_merge_graphs(graphs, clusters):
    # Here, we only merge nodes that don't conflict

    # merge graphs
    merged_G = nx.compose_all(graphs)
    node_count = max(merged_G.nodes()) + 1

    for cluster in clusters:

        # check if there are any to collapse
        if len(cluster) <= 1: continue

        # check for conflicts
        seen = merged_G.nodes[cluster[0]]['members'].copy()
        noconflict = True
        for n in cluster[1:]:
            if not seen.isdisjoint(merged_G.nodes[n]['members']):
                noconflict = False
                break
            seen |= merged_G.nodes[n]['members']

        if noconflict:
            # no conflicts so merge
            node_count += 1
            merged_G = merge_node_cluster(merged_G,
                                          cluster,
                                          node_count,
                                          multi_centroid=True,
                                          check_merge_mems=True)

    return merged_G 

def test_input_output():
    l = [nx.Graph([(1,2)]),nx.Graph([(3,4)])]
    U = nx.disjoint_union_all(l)
    assert_equal(len(l),2)
    C = nx.compose_all(l)
    assert_equal(len(l),2)
    l = [nx.Graph([(1,2)]),nx.Graph([(1,2)])]
    R = nx.intersection_all(l)
    assert_equal(len(l),2) 

def test_mixed_type_compose():
    G = nx.Graph()
    H = nx.MultiGraph()
    I = nx.Graph()
    U = nx.compose_all([G,H,I]) 

def test_input_output():
    l = [nx.Graph([(1, 2)]), nx.Graph([(3, 4)])]
    U = nx.disjoint_union_all(l)
    assert_equal(len(l), 2)
    C = nx.compose_all(l)
    assert_equal(len(l), 2)
    l = [nx.Graph([(1, 2)]), nx.Graph([(1, 2)])]
    R = nx.intersection_all(l)
    assert_equal(len(l), 2) 

def test_mixed_type_compose():
    G = nx.Graph()
    H = nx.MultiGraph()
    I = nx.Graph()
    U = nx.compose_all([G, H, I]) 

def test_empty_compose_all():
    nx.compose_all([]) 

def test_input_output():
    l = [nx.Graph([(1,2)]),nx.Graph([(3,4)])]
    U = nx.disjoint_union_all(l)
    assert_equal(len(l),2)
    C = nx.compose_all(l)
    assert_equal(len(l),2)
    l = [nx.Graph([(1,2)]),nx.Graph([(1,2)])]
    R = nx.intersection_all(l)
    assert_equal(len(l),2) 

def test_mixed_type_compose():
    G = nx.Graph()
    H = nx.MultiGraph()
    I = nx.Graph()
    U = nx.compose_all([G,H,I]) 

def test_union_all_and_compose_all():
    K3=nx.complete_graph(3)
    P3=nx.path_graph(3)

    G1=nx.DiGraph()
    G1.add_edge('A','B')
    G1.add_edge('A','C')
    G1.add_edge('A','D')
    G2=nx.DiGraph()
    G2.add_edge('1','2')
    G2.add_edge('1','3')
    G2.add_edge('1','4')

    G=nx.union_all([G1,G2])
    H=nx.compose_all([G1,G2])
    assert_edges_equal(G.edges(),H.edges())
    assert_false(G.has_edge('A','1'))
    assert_raises(nx.NetworkXError, nx.union, K3, P3)
    H1=nx.union_all([H,G1],rename=('H','G1'))
    assert_equal(sorted(H1.nodes()),
        ['G1A', 'G1B', 'G1C', 'G1D',
         'H1', 'H2', 'H3', 'H4', 'HA', 'HB', 'HC', 'HD'])

    H2=nx.union_all([H,G2],rename=("H",""))
    assert_equal(sorted(H2.nodes()),
        ['1', '2', '3', '4',
         'H1', 'H2', 'H3', 'H4', 'HA', 'HB', 'HC', 'HD'])

    assert_false(H1.has_edge('NB','NA'))

    G=nx.compose_all([G,G])
    assert_edges_equal(G.edges(),H.edges())

    G2=nx.union_all([G2,G2],rename=('','copy'))
    assert_equal(sorted(G2.nodes()),
        ['1', '2', '3', '4', 'copy1', 'copy2', 'copy3', 'copy4'])

    assert_equal(G2.neighbors('copy4'),[])
    assert_equal(sorted(G2.neighbors('copy1')),['copy2', 'copy3', 'copy4'])
    assert_equal(len(G),8)
    assert_equal(nx.number_of_edges(G),6)

    E=nx.disjoint_union_all([G,G])
    assert_equal(len(E),16)
    assert_equal(nx.number_of_edges(E),12)

    E=nx.disjoint_union_all([G1,G2])
    assert_equal(sorted(E.nodes()),[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11])

    G1=nx.DiGraph()
    G1.add_edge('A','B')
    G2=nx.DiGraph()
    G2.add_edge(1,2)
    G3=nx.DiGraph()
    G3.add_edge(11,22)
    G4=nx.union_all([G1,G2,G3],rename=("G1","G2","G3"))
    assert_equal(sorted(G4.nodes()),
        ['G1A', 'G1B', 'G21', 'G22',
         'G311', 'G322']) 

def test_union_all_and_compose_all():
    K3 = nx.complete_graph(3)
    P3 = nx.path_graph(3)

    G1 = nx.DiGraph()
    G1.add_edge('A', 'B')
    G1.add_edge('A', 'C')
    G1.add_edge('A', 'D')
    G2 = nx.DiGraph()
    G2.add_edge('1', '2')
    G2.add_edge('1', '3')
    G2.add_edge('1', '4')

    G = nx.union_all([G1, G2])
    H = nx.compose_all([G1, G2])
    assert_edges_equal(G.edges(), H.edges())
    assert_false(G.has_edge('A', '1'))
    assert_raises(nx.NetworkXError, nx.union, K3, P3)
    H1 = nx.union_all([H, G1], rename=('H', 'G1'))
    assert_equal(sorted(H1.nodes()),
                 ['G1A', 'G1B', 'G1C', 'G1D',
                  'H1', 'H2', 'H3', 'H4', 'HA', 'HB', 'HC', 'HD'])

    H2 = nx.union_all([H, G2], rename=("H", ""))
    assert_equal(sorted(H2.nodes()),
                 ['1', '2', '3', '4',
                  'H1', 'H2', 'H3', 'H4', 'HA', 'HB', 'HC', 'HD'])

    assert_false(H1.has_edge('NB', 'NA'))

    G = nx.compose_all([G, G])
    assert_edges_equal(G.edges(), H.edges())

    G2 = nx.union_all([G2, G2], rename=('', 'copy'))
    assert_equal(sorted(G2.nodes()),
                 ['1', '2', '3', '4', 'copy1', 'copy2', 'copy3', 'copy4'])

    assert_equal(sorted(G2.neighbors('copy4')), [])
    assert_equal(sorted(G2.neighbors('copy1')), ['copy2', 'copy3', 'copy4'])
    assert_equal(len(G), 8)
    assert_equal(nx.number_of_edges(G), 6)

    E = nx.disjoint_union_all([G, G])
    assert_equal(len(E), 16)
    assert_equal(nx.number_of_edges(E), 12)

    E = nx.disjoint_union_all([G1, G2])
    assert_equal(sorted(E.nodes()), [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11])

    G1 = nx.DiGraph()
    G1.add_edge('A', 'B')
    G2 = nx.DiGraph()
    G2.add_edge(1, 2)
    G3 = nx.DiGraph()
    G3.add_edge(11, 22)
    G4 = nx.union_all([G1, G2, G3], rename=("G1", "G2", "G3"))
    assert_equal(sorted(G4.nodes()),
                 ['G1A', 'G1B', 'G21', 'G22',
                  'G311', 'G322']) 

def test_union_all_and_compose_all():
    K3=nx.complete_graph(3)
    P3=nx.path_graph(3)

    G1=nx.DiGraph()
    G1.add_edge('A','B')
    G1.add_edge('A','C')
    G1.add_edge('A','D')
    G2=nx.DiGraph()
    G2.add_edge('1','2')
    G2.add_edge('1','3')
    G2.add_edge('1','4')

    G=nx.union_all([G1,G2])
    H=nx.compose_all([G1,G2])
    assert_edges_equal(G.edges(),H.edges())
    assert_false(G.has_edge('A','1'))
    assert_raises(nx.NetworkXError, nx.union, K3, P3)
    H1=nx.union_all([H,G1],rename=('H','G1'))
    assert_equal(sorted(H1.nodes()),
        ['G1A', 'G1B', 'G1C', 'G1D',
         'H1', 'H2', 'H3', 'H4', 'HA', 'HB', 'HC', 'HD'])

    H2=nx.union_all([H,G2],rename=("H",""))
    assert_equal(sorted(H2.nodes()),
        ['1', '2', '3', '4',
         'H1', 'H2', 'H3', 'H4', 'HA', 'HB', 'HC', 'HD'])

    assert_false(H1.has_edge('NB','NA'))

    G=nx.compose_all([G,G])
    assert_edges_equal(G.edges(),H.edges())

    G2=nx.union_all([G2,G2],rename=('','copy'))
    assert_equal(sorted(G2.nodes()),
        ['1', '2', '3', '4', 'copy1', 'copy2', 'copy3', 'copy4'])

    assert_equal(sorted(G2.neighbors('copy4')),[])
    assert_equal(sorted(G2.neighbors('copy1')),['copy2', 'copy3', 'copy4'])
    assert_equal(len(G),8)
    assert_equal(nx.number_of_edges(G),6)

    E=nx.disjoint_union_all([G,G])
    assert_equal(len(E),16)
    assert_equal(nx.number_of_edges(E),12)

    E=nx.disjoint_union_all([G1,G2])
    assert_equal(sorted(E.nodes()),[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11])

    G1=nx.DiGraph()
    G1.add_edge('A','B')
    G2=nx.DiGraph()
    G2.add_edge(1,2)
    G3=nx.DiGraph()
    G3.add_edge(11,22)
    G4=nx.union_all([G1,G2,G3],rename=("G1","G2","G3"))
    assert_equal(sorted(G4.nodes()),
        ['G1A', 'G1B', 'G21', 'G22',
         'G311', 'G322'])