def ring(N, R):
# Create glias ring
g1 = nx.cycle_graph(N)
for glia in range(0, N):
for r in range(1, R + 1):
k = glia + r
if k > N - 1:
k = k - N
g1.add_edge(glia, k)
k = glia - r
if k < 0:
k = k + N
g1.add_edge(glia, k)
# Create neurons ring
g2 = nx.cycle_graph(N)
# Create inter adjacency matrix
adj_block = mx.lil_matrix(np.zeros((N * 2, N * 2)))
adj_block[0:N, N:2 * N] = np.identity(N)
adj_block += adj_block.T
mg = mx.MultilayerGraph(list_of_layers=[g1, g2],
inter_adjacency_matrix=adj_block)
return mg
def build_mx_multigraph(func_mat, dwi_mat, name, namer_dir):
"""
It creates a symmetric (undirected) MultilayerGraph object from
vertex-aligned structural and functional connectivity matrices.
Parameters:
-----------
func_mat : ndarray
Functional adjacency matrix of size N x N.
dwi_mat : ndarray
Structural adjacency matrix of size N x N.
name : str
Intended name of the multiplex object.
namer_dir : str
Path to output directory.
Returns:
--------
mg_path : str
A filepath to a gpickled MultilayerGraph object
References
----------
.. [1] R. Amato, N. E Kouvaris, M. San Miguel and A. Diaz-Guilera,
Opinion competition dynamics on multiplex networks, New J. Phys.
DOI: https://doi.org/10.1088/1367-2630/aa936a
.. [2] N. E. Kouvaris, S. Hata and A. Diaz-Guilera, Pattern formation
in multiplex networks, Scientific Reports 5, 10840 (2015).
http://www.nature.com/srep/2015/150604/srep10840/full/srep10840.html
.. [3] A. Sole-Ribata, M. De Domenico, N. E. Kouvaris, A. Diaz-Guilera, S.
Gomez and A. Arenas, Spectral properties of the Laplacian of a multiplex
network, Phys. Rev. E 88, 032807 (2013).
http://journals.aps.org/pre/abstract/10.1103/PhysRevE.88.032807
"""
import networkx as nx
import multinetx as mx
import pickle5 as pickle
mg = mx.MultilayerGraph()
N = dwi_mat.shape[0]
adj_block = mx.lil_matrix(np.zeros((N * 2, N * 2)))
adj_block[0:N, N:2 * N] = np.identity(N)
adj_block += adj_block.T
G_dwi = nx.from_numpy_matrix(dwi_mat)
G_func = nx.from_numpy_matrix(func_mat)
mg.add_layer(G_dwi)
mg.add_layer(G_func)
mg.layers_interconnect(inter_adjacency_matrix=adj_block)
mg.name = name
# Save mG to pickle
graph_dir = f"{namer_dir}/mplx_graphs"
if not os.path.isdir(graph_dir):
os.mkdir(graph_dir)
mG_path = f"{graph_dir}/{name}.pkl"
nx.write_gpickle(mg, mG_path, protocol=2)
return mG_path
def test_plot_all_struct_func(plotting_data):
"""Test structural and functional plotting."""
import multinetx as mx
base_dir = str(Path(__file__).parent / "examples")
temp_dir = tempfile.TemporaryDirectory()
dir_path = str(temp_dir.name)
labels = plotting_data['labels'][:10]
coords = plotting_data['coords'][:10]
metadata = {'coords': coords, 'labels': labels}
name = 'output_fname'
func_file = (
f"{base_dir}/miscellaneous/graphs/002_modality-func_rsn-Default_roi-002_parcels_re"
f"sampled2roimask_pDMN_3_bin_raw_est-sps_nodetype-spheres-6mm_smooth-2fwhm_hpass-"
f"FalseHz_raw.npy")
dwi_file = (
f"{base_dir}/miscellaneous/graphs/002_modality-dwi_rsn-Default_roi-002_parcels_res"
f"ampled2roimask_pDMN_3_bin_raw_est-sps_parc_samples-2streams_tt-local_dg-prob_ml-"
f"200_raw.npy")
modality_paths = (func_file, dwi_file)
G_func = nx.from_numpy_matrix(np.load(func_file))
G_dwi = nx.from_numpy_matrix(np.load(dwi_file))
mG_path = tempfile.NamedTemporaryFile(mode='w+', suffix='.gpickle')
mG = mx.MultilayerGraph(list_of_layers=[G_func, G_dwi])
# This is a hack to get i/o working. There is an nx inhertiance issue that prevents reading.
intra_layer_edges = mG.intra_layer_edges
del mG.intra_layer_edges
nx.write_gpickle(mG, mG_path.name)
plot_gen.plot_all_struct_func(mG_path.name, dir_path, name, modality_paths,
metadata)
temp_dir.cleanup()
mG_path.close()
import numpy as np
import matplotlib.pyplot as plt
import multinetx as mx
N = 10
g1 = mx.erdos_renyi_graph(N, 0.07, seed=218)
g2 = mx.erdos_renyi_graph(N, 0.07, seed=211)
adj_block = mx.lil_matrix(np.zeros((N * 2, N * 2)))
adj_block[0:N, N:2 * N] = np.identity(N) # L_12
adj_block += adj_block.T
mg = mx.MultilayerGraph(list_of_layers=[g1, g2],
inter_adjacency_matrix=adj_block)
mg.set_edges_weights(inter_layer_edges_weight=2)
mg.set_intra_edges_weights(layer=0, weight=1)
mg.set_intra_edges_weights(layer=1, weight=2)
fig = plt.figure(figsize=(10, 10))
ax1 = fig.add_subplot(122)
ax1.axis('off')
ax1.set_title('regular interconnected network')
pos = mx.get_position(mg,
mx.fruchterman_reingold_layout(mg.get_layer(0)),
layer_vertical_shift=1.4,
layer_horizontal_shift=0.0,
proj_angle=7)
import multinetx as mx
import numpy as np
import matplotlib.pyplot as plt
N = 50
g1 = mx.erdos_renyi_graph(N, 0.07, seed=218)
g2 = mx.erdos_renyi_graph(N, 0.07, seed=211)
g3 = mx.erdos_renyi_graph(N, 0.07, seed=208)
mg = mx.MultilayerGraph(list_of_layers=[g1, g2, g3])
mg.set_intra_edges_weights(layer=0, weight=1)
mg.set_intra_edges_weights(layer=1, weight=2)
mg.set_intra_edges_weights(layer=2, weight=3)
fig = plt.figure(figsize=(15, 5))
ax2 = fig.add_subplot(122)
ax2.axis('off')
ax2.set_title('edge colored network')
pos = mx.get_position(mg,
mx.fruchterman_reingold_layout(g1),
layer_vertical_shift=0.2,
layer_horizontal_shift=0.0,
proj_angle=47)
mx.draw_networkx(mg,
pos=pos,
ax=ax2,
node_size=50,
with_labels=False,
edge_color=[mg[a][b]['weight'] for a, b in mg.edges()],
edge_cmap=plt.cm.jet_r)
def main():
data = collect_data('results/t6/')
comm = collect_community('results/t6/')
def find_best(data, method):
key = max(data[method].iteritems(), key=operator.itemgetter(1))[0]
y = data[method][key]
return y, key, method
print 'LART', data['lart']['9.0_1.0_1.0']
print 'PMM', data['pmm']['30.0_140.0']
print 'Glouvain', data['glouvain']['1.0_1.0']
gl = find_best(data, 'glouvain')
ll = find_best(data, 'lart')
pl = find_best(data, 'pmm')
print 'LART', ll
print 'PMM', pl
print 'Glouvain', gl
best = max([gl, ll, pl], key=operator.itemgetter(0))
best_comm = {}
for b in comm[best[2]][best[1]].split('\n'):
if b:
a, l, c = b.split(',')
best_comm['%s-%s' % (a, l)] = int(c)
layers = {'RT': nx.Graph(), 'ff': nx.Graph(), 'Re': nx.Graph()}
ids = {}
counter = 0
groups = []
with open('data/t6/dk', 'r') as fd:
for l in fd.readlines():
a1, a2, layer = l.replace('\n', '').split(",")
if a1 not in ids:
ids[a1] = counter
counter = counter + 1
if a2 not in ids:
ids[a2] = counter
counter = counter + 1
groups.append(best_comm['%s-%s' % (a1, layer)])
groups.append(best_comm['%s-%s' % (a2, layer)])
for k, v in layers.iteritems():
v.add_node(ids[a1], label=best_comm['%s-%s' % (a1, layer)])
v.add_node(ids[a2], label=best_comm['%s-%s' % (a2, layer)])
layers[layer].add_edge(ids[a1], ids[a2])
truth = {}
with open('data/t6/dk_truth', 'r') as fd:
for l in fd.readlines():
actor, party = l.replace('\n', '').split(',')
truth[actor] = party
mapping = dict(zip(sorted(groups), count()))
N, L = len(layers['ff'].nodes()), len(layers.keys())
adj_block = mx.lil_matrix(np.zeros((N * L, N * L)))
for i in xrange(L):
for j in xrange(L):
if i < j:
adj_block[N * i:N * (i + 1),
N * j:(j + 1) * N] = np.identity(N)
adj_block += adj_block.T
mg = mx.MultilayerGraph(list_of_layers=[v for k, v in layers.items()])
#inter_adjacency_matrix = adj_block)
mg.set_edges_weights(intra_layer_edges_weight=1)
#inter_layer_edges_weight=2)
fig = plt.figure(figsize=(16, 16))
plt.title('Twitter data of the Danish 2015 election')
stats = collections.defaultdict(list)
for k, v in best_comm.items():
stats[v].append(k)
stats2 = collections.defaultdict(dict)
for k, v in stats.items():
for e in v:
actor, _ = e.split('-')
if truth[actor] in stats2[k]:
stats2[k][truth[actor]] += 1
else:
stats2[k][truth[actor]] = 1
left = [
'Dansk Folkeparti',
'Venstre',
'Liberal Alliance',
'Det Konservative Folkeparti',
'KristenDemokraterne',
]
right = [
'Socialistisk Folkeparti', 'Radikale Venstre', 'Socialdemokratiet',
'Alternativet', 'Enhedslisten'
]
out = 'Udenfor partierne'
for k, v in stats2.items():
total = 0
for k1, v1 in v.items():
total += v1
pscore = 0
for k1, v1 in v.items():
if k1 in left:
pscore += (stats2[k][k1] * 1)
if k1 in right:
pscore -= (stats2[k][k1] * 1)
stats2[k][k1] = round(float(v1) / float(total), 2)
stats2[k]['nodes'] = filter(
lambda x, i=mg, k=k: i.node[x]['label'] == k, mg.node)
stats2[k]['pscore'] = pscore / float(total)
stats2 = dict(stats2)
if len(sys.argv) > 1 and sys.argv[1] == 'heat':
cmap = plt.get_cmap('RdBu_r')
colors = [stats2[mg.node[n]['label']]['pscore'] for n in mg.nodes()]
pos = mx.get_position(mg,
nx.spring_layout(layers[layers.keys()[2]],
weight='pscore'),
layer_vertical_shift=0.2,
layer_horizontal_shift=0.0,
proj_angle=47)
for key, val in stats2.items():
set_trace()
mx.draw_networkx_nodes(mg,
pos=pos,
node_size=100,
with_labels=False,
nodelist=val['nodes'],
label=key,
node_color=[colors[n] for n in val['']],
cmap=cmap)
else:
val_map = {
0: 'k',
1: 'r',
2: 'g',
3: 'b',
4: 'c',
5: 'm',
6: 'y',
7: '0.75',
8: 'w',
}
colors = [val_map[mg.node[n]['label']] for n in mg.nodes()]
pos = mx.get_position(mg,
nx.spring_layout(layers[layers.keys()[2]]),
layer_vertical_shift=0.2,
layer_horizontal_shift=0.0,
proj_angle=47)
for k, v in stats2.items():
mx.draw_networkx_nodes(mg,
pos=pos,
node_size=100,
with_labels=False,
nodelist=v['nodes'],
label=k,
node_color=[colors[n] for n in v['nodes']],
cmap=plt.get_cmap('Set2'))
mx.draw_networkx_edges(mg, pos=pos, edge_color='b')
fig.tight_layout()
plt.legend(numpoints=1, loc=1)
plt.xticks([])
plt.yticks([])
plt.show()
def multilayer(self, filename='multilayer_network'):
import numpy as np
import matplotlib.pyplot as plt
import multinetx as mx
import networkx as nx
from mpl_toolkits.basemap import Basemap
# %% Define the type of interconnection between the layers
N = len(self.poi_nodes) + len(self.user_nodes)
N1 = len(self.poi_nodes)
adj_block = mx.lil_matrix(np.zeros((N, N)))
for row in self.user_poi_s.iterrows():
user_ind = self.user_nodes[self.user_nodes['userId'] == row[1]
['userId']].index[0]
pos_ind = self.poi_nodes[self.poi_nodes['venueId'] == row[1]
['venueId']].index[0]
adj_block[pos_ind, user_ind] = row[1]['weight']
adj_block += adj_block.T
# %% multilayer network
poi_layer = nx.Graph(layer='POI')
poi_layer.add_nodes_from(self.poi_nodes.index.values)
poi_layer.add_weighted_edges_from(self.poi_edges)
user_layer = nx.DiGraph(layer='User')
user_layer.add_nodes_from(self.user_nodes.index.values)
user_layer.add_weighted_edges_from(self.user_edges)
mg = mx.MultilayerGraph(list_of_layers=[poi_layer, user_layer],
inter_adjacency_matrix=adj_block)
# venue position in decimal lat/lon
lats_v = list(self.poi_nodes['latitude'])
lons_v = list(self.poi_nodes['longitude'])
min_lat = min(lats_v)
max_lat = max(lats_v)
min_lon = min(lons_v)
max_lon = max(lons_v)
# user position in decimal lat/lon
lats_u = list(self.user_nodes['latitude'])
lons_u = list(self.user_nodes['longitude'])
min_lat = min(min_lat, min(lats_u))
max_lat = max(max_lat, max(lats_u))
min_lon = min(min_lon, min(lons_u))
max_lon = max(max_lon, max(lons_u))
m = Basemap(projection='merc',
llcrnrlon=min_lon,
llcrnrlat=min_lat,
urcrnrlon=max_lon,
urcrnrlat=max_lat,
lat_ts=0,
resolution='i',
suppress_ticks=True)
# convert lat and lon to map projection
x, y = m(lons_v, lats_v)
ppos = {}
n = 0
for v in self.poi_nodes.index:
ppos[v] = np.asarray([x[n], y[n]])
n += 1
# convert lat and lon to map projection
x, y = m(lons_u, lats_u)
n = 0
for v in self.user_nodes.index:
ppos[v] = np.asarray([x[n], y[n]])
n += 1
target_userID = list(self.similar_users['userId1'])[0]
node_of_target_user = self.user_nodes[self.user_nodes['userId'] ==
target_userID].index[0]
for i in range(2):
pos = mx.get_position(mg,
ppos,
layer_vertical_shift=1000.0,
layer_horizontal_shift=400.0,
proj_angle=0.2)
fig, ax2 = plt.subplots(figsize=(10, 5))
# ax2.axis('off')
ax2.set_title(
'Multilayer Network of User and PoI (Target User ID: {0})'.
format(target_userID))
mg.set_edges_weights(inter_layer_edges_weight=3)
mg.set_intra_edges_weights(layer=0, weight=5)
# mg.set_intra_edges_weights(layer=1,weight=2)
mx.draw_networkx(
mg,
pos=pos,
ax=ax2,
node_size=50,
with_labels=False,
node_color=[
'y' if a < N1 else
('brown' if a == node_of_target_user else 'g')
for a in mg.nodes()
],
edge_color=[mg[a][b]['weight'] for a, b in mg.edges()],
edge_cmap=plt.cm.Blues)
# plt.show()
plt.savefig('output/{0}.png'.format(filename),
dpi=500,
bbox_inches='tight')
pos_ind = poi_nodes[poi_nodes['venueId'] == row[1]['venueId']].index[0]
adj_block[pos_ind, user_ind] = row[1]['weight']
adj_block += adj_block.T
# %% multilayer network
poi_layer = nx.Graph(layer='POI')
poi_layer.add_nodes_from(poi_nodes.index.values)
poi_layer.add_weighted_edges_from(poi_edges)
user_layer = nx.DiGraph(layer='User')
user_layer.add_nodes_from(user_nodes.index.values)
user_layer.add_weighted_edges_from(user_edges)
mg = mx.MultilayerGraph(list_of_layers=[poi_layer,user_layer], inter_adjacency_matrix=adj_block)
m = Basemap(
projection='merc',
llcrnrlon=lon1,
llcrnrlat=lat1,
urcrnrlon=lon2,
urcrnrlat=lat2,
lat_ts=0,
resolution='i',
suppress_ticks=True)
# position in decimal lat/lon
lats=list(poi_nodes['latitude'])
lons=list(poi_nodes['longitude'])
# convert lat and lon to map projection