# mnet[p, layer_name][j, layer_name] = 1
# for p in node_set:
# if p in home_set and p in school_set:
# mnet[p, 'Households'][p, 'Schools'] = 1
# if p in home_set and p in work_set:
# mnet[p, 'Households'][p, 'Work'] = 1
# nn = mnet.iter_nodes('Households')
# for i in nn:
# print(i)
# pos = nx.nx_pydot.graphviz_layout(G, prog='pydot')
# print(pos)
# print(A.layout())
import pydot
# P = nx.nx_pydot.to_pydot(G)
# print(P)
nx.nx_pydot.pydot_layout(G, prog='neato')
fig = pymnet.draw(
mnet,
defaultLayerAlpha=0.3,
layout='circular',
# nodeCoords = pos,
nodeLabelRule={})
# fig.savefig('net.pdf')
fig.savefig('net_2.pdf')
def plot_complete_invariant_average_time_series(subnet_filename_list,
title,
xlabel,
ylabel,
savename=None,
examples_filename=None,
map_ni_to_nli=False,
yscale='log',
colormap=plt.cm.jet,
**kwargs):
compinv_timeseries_dict_list = []
layersets = set()
invariants = set()
for filename in subnet_filename_list:
f = open(filename, 'r')
complete_invariant_timeseries_dict = pickle.load(f)
f.close()
for key in complete_invariant_timeseries_dict:
invariants.add(key)
layersets.update(
[key2 for key2 in complete_invariant_timeseries_dict[key]])
compinv_timeseries_dict_list.append(complete_invariant_timeseries_dict)
if examples_filename is not None:
invdicts = complete_invariant_dicts.load_example_nets_file(
examples_filename)
else:
nnodes = int(subnet_filename_list[0].split('/')[-1].strip()[0])
nlayers = int(subnet_filename_list[0].split('/')[-1].strip()[2])
example_nets_filename = 'example_nets/' + str(nnodes) + '_' + str(
nlayers) + '.pickle'
invdicts = complete_invariant_dicts.load_example_nets_file(
example_nets_filename)
layersets = list(layersets)
layersets.sort()
full_range = zip(*(range(layersets[0][0], layersets[-1][-1] + 1)[ii:]
for ii in range(len(layersets[0]))))
if layersets != full_range:
layersets = full_range
x_axis = list(range(layersets[0][0], layersets[-1][1]))
if map_ni_to_nli:
invariants = set()
mapped_invdicts = dict()
mapped_compinv_timeseries_dict_list = []
for complete_invariant_timeseries_dict in compinv_timeseries_dict_list:
mapped_complete_invariant_timeseries_dict = dict()
for complete_invariant in complete_invariant_timeseries_dict:
nl_complete_invariant = pn.get_complete_invariant(
invdicts[complete_invariant])
if nl_complete_invariant not in mapped_invdicts:
mapped_invdicts[nl_complete_invariant] = invdicts[
complete_invariant]
invariants.add(nl_complete_invariant)
mapped_complete_invariant_timeseries_dict[
nl_complete_invariant] = mapped_complete_invariant_timeseries_dict.get(
nl_complete_invariant, dict())
for tw in complete_invariant_timeseries_dict[
complete_invariant]:
mapped_complete_invariant_timeseries_dict[
nl_complete_invariant][
tw] = mapped_complete_invariant_timeseries_dict[
nl_complete_invariant].get(
tw,
0) + complete_invariant_timeseries_dict[
complete_invariant][tw]
mapped_compinv_timeseries_dict_list.append(
mapped_complete_invariant_timeseries_dict)
compinv_timeseries_dict_list = mapped_compinv_timeseries_dict_list
invdicts = mapped_invdicts
number_of_invariants = len(invariants)
grid_side_length = 0
while grid_side_length**2 < number_of_invariants:
grid_side_length = grid_side_length + 1
ax_locs = list(
itertools.product(range(grid_side_length),
range(grid_side_length, 2 * grid_side_length)))
fig = plt.figure(figsize=(12, 6))
main_ax = plt.subplot2grid((grid_side_length, 2 * grid_side_length),
(0, 0),
rowspan=grid_side_length,
colspan=grid_side_length)
colorcycler = plt.cycler('color',
colormap(np.linspace(0, 1, number_of_invariants)))
main_ax.set_prop_cycle(colorcycler)
for ii, compinv in enumerate(sorted(invariants)):
y_values = []
std_values = []
for layerset in layersets:
temp_layerset_vals = []
for compinv_timeseries_dict in compinv_timeseries_dict_list:
if compinv in compinv_timeseries_dict:
temp_layerset_vals.append(
compinv_timeseries_dict[compinv].get(layerset, 0))
else:
temp_layerset_vals.append(0)
y_values.append(np.mean(temp_layerset_vals))
std_values.append(np.std(temp_layerset_vals))
line = main_ax.plot(x_axis, y_values, label=str(ii))
main_ax.fill_between(x_axis,
np.subtract(y_values, std_values),
np.add(y_values, std_values),
facecolor=line[0].get_color(),
alpha=0.2)
compinv_ax = plt.subplot2grid((grid_side_length, 2 * grid_side_length),
ax_locs[ii],
projection='3d')
M = invdicts[compinv]
pn.draw(M,
layout='shell',
alignedNodes=True,
ax=compinv_ax,
layerLabelRule={},
nodeLabelRule={})
if grid_side_length < 3:
legend_loc = 'lower left'
else:
legend_loc = (0, 0)
leg = compinv_ax.legend(labels=[''],
loc=legend_loc,
handles=line,
frameon=False)
plt.setp(leg.get_lines(), linewidth=4)
main_ax.set_xticks(x_axis)
main_ax.set_xticklabels(layersets, rotation=90, fontsize='small')
main_ax.set_yscale(yscale)
main_ax.set_xlabel(xlabel)
main_ax.set_ylabel(ylabel)
main_ax.set_title(title)
main_ax.margins(y=0.2)
main_ax.set_xlim([x_axis[0], x_axis[-1]])
plt.tight_layout()
if savename == None:
plt.show()
else:
plt.savefig(savename, format='pdf')
fig = pymnet.draw(
net,
show=False,
azim=-60,
elev=25,
layergap=0.75,
layout='shell',
# layershape='circle',
autoscale=True,
defaultNodeLabelAlpha=0.75,
defaultLayerAlpha=0.25,
# color
nodeColorDict=nodeColorDict0,
nodeLabelColorDict=nodeColorDict0,
edgeColorDict=edgeColorDict0,
# size
nodeSizeDict=nodeSizeDict0,
nodeSizeRule={
'scalecoeff': 0.2,
'rule': 'scaled'
},
nodeLabelSizeDict=nodeLabelSizeDict0,
# width
edgeWidthDict=edgeWidthDict0,
defaultEdgeAlpha=1,
# coords
nodeCoords=nodeCoords0,
nodelayerCoords=nodeCoords0,
layerColorDict={
'Gene': '#DAA520',
'Protein': '#FF0000'
},
layerOrderDict={
'SNP': 4,
'Gene': 3,
'miRNA': 2,
'Protein': 1
},
# node label style
defaultNodeLabelStyle='oblique', # normal, italic or oblique
layerPadding=0.25)
def plot_complete_invariant_time_series(subnet_filename,
title,
xlabel,
ylabel,
savename=None,
examples_filename=None,
map_ni_to_nli=False,
colormap=plt.cm.jet,
**kwargs):
M = pn.MultilayerNetwork(aspects=1, fullyInterconnected=False)
M['a', 'b', 0, 0] = 1
M['a', 'a', 0, 1] = 1
#layersetwise_complete_invariants = dict()
complete_invariant_timeseries_dict = dict()
layersets = set()
invariants = set()
if subnet_filename.strip()[-10:] == 'agg.pickle':
f = open(subnet_filename, 'r')
complete_invariant_timeseries_dict = pickle.load(f)
f.close()
for key in complete_invariant_timeseries_dict:
invariants.add(key)
layersets.update(
[key2 for key2 in complete_invariant_timeseries_dict[key]])
else:
for subnet_data in subgraph_classification.yield_subnet_with_complete_invariant(
subnet_filename):
nodes = tuple(subnet_data[0])
layers = tuple(sorted(subnet_data[1]))
complete_invariant = subnet_data[2]
layersets.add(layers)
invariants.add(complete_invariant)
#layersetwise_complete_invariants[layers] = layersetwise_complete_invariants.get(layers,dict())
#layersetwise_complete_invariants[layers][complete_invariant] = layersetwise_complete_invariants[layers].get(complete_invariant,0) + 1
complete_invariant_timeseries_dict[
complete_invariant] = complete_invariant_timeseries_dict.get(
complete_invariant, dict())
complete_invariant_timeseries_dict[complete_invariant][
layers] = complete_invariant_timeseries_dict[
complete_invariant].get(layers, 0) + 1
layersets = list(layersets)
layersets.sort()
full_range = zip(*(range(layersets[0][0], layersets[-1][-1] + 1)[ii:]
for ii in range(len(layersets[0]))))
if layersets != full_range:
layersets = full_range
x_axis = list(range(layersets[0][0], layersets[-1][1]))
# load example networks
if examples_filename is not None:
f = open(examples_filename, 'r')
invdicts = pickle.load(f)
f.close()
else:
nnodes = int(subnet_filename.split('/')[-1].strip()[0])
nlayers = int(subnet_filename.split('/')[-1].strip()[2])
example_nets_filename = 'example_nets/' + str(nnodes) + '_' + str(
nlayers) + '.pickle'
invdicts = complete_invariant_dicts.load_example_nets_file(
example_nets_filename)
# map node isomorphisms to nodelayer isomorphisms:
if map_ni_to_nli:
invariants = set()
mapped_invdicts = dict()
mapped_complete_invariant_timeseries_dict = dict()
for complete_invariant in complete_invariant_timeseries_dict:
nl_complete_invariant = pn.get_complete_invariant(
invdicts[complete_invariant])
if nl_complete_invariant not in mapped_invdicts:
mapped_invdicts[nl_complete_invariant] = invdicts[
complete_invariant]
invariants.add(nl_complete_invariant)
mapped_complete_invariant_timeseries_dict[
nl_complete_invariant] = mapped_complete_invariant_timeseries_dict.get(
nl_complete_invariant, dict())
for tw in complete_invariant_timeseries_dict[complete_invariant]:
mapped_complete_invariant_timeseries_dict[
nl_complete_invariant][
tw] = mapped_complete_invariant_timeseries_dict[
nl_complete_invariant].get(
tw, 0) + complete_invariant_timeseries_dict[
complete_invariant][tw]
complete_invariant_timeseries_dict = mapped_complete_invariant_timeseries_dict
invdicts = mapped_invdicts
# needed numbers of example figures
number_of_invariants = len(invariants)
grid_side_length = 0
while grid_side_length**2 < number_of_invariants:
grid_side_length = grid_side_length + 1
ax_locs = list(
itertools.product(range(grid_side_length),
range(grid_side_length, 2 * grid_side_length)))
# figure
fig = plt.figure(figsize=(12, 6))
main_ax = plt.subplot2grid((grid_side_length, 2 * grid_side_length),
(0, 0),
rowspan=grid_side_length,
colspan=grid_side_length)
colorcycler = plt.cycler('color',
colormap(np.linspace(0, 1, number_of_invariants)))
main_ax.set_prop_cycle(colorcycler)
# side_ax = plt.subplot2grid((2,4),(0,2),projection='3d')
# side_ax2 = plt.subplot2grid((2,4),(0,3),projection='3d')
#plt.hold(True)
# identifiers for legend
ids = range(len(invariants))
for ii, compinv in enumerate(
sorted(complete_invariant_timeseries_dict.iterkeys())):
y_values = []
for layerset in layersets:
y_values.append(complete_invariant_timeseries_dict[compinv].get(
layerset, 0))
#main_ax = plt.subplot2grid((2,4),(0,0),rowspan=2,colspan=2)
#main_ax.plot(x_axis,y_values,label=str(compinv))
line = main_ax.plot(x_axis, y_values, label=str(ii))
compinv_ax = plt.subplot2grid((grid_side_length, 2 * grid_side_length),
ax_locs[ii],
projection='3d')
#example_ax = plt.gcf().add_axes((1.1,0,0.5,0.5),projection='3d')
M = invdicts[compinv]
pn.draw(M,
layout='shell',
alignedNodes=True,
ax=compinv_ax,
layerLabelRule={},
nodeLabelRule={})
#compinv_ax.text2D(0,0,str(ii),None,False,transform=compinv_ax.transAxes)
if grid_side_length < 3:
legend_loc = 'lower left'
else:
legend_loc = (0, 0)
leg = compinv_ax.legend(labels=[''],
loc=legend_loc,
handles=line,
frameon=False)
plt.setp(leg.get_lines(), linewidth=4)
# if ii==0:
# pn.draw(M,ax=side_ax)
# else:
# pn.draw(M,ax=side_ax2)
#plt.sca(fig.gca())
# plt.xticks(x_axis,layersets,rotation=90,fontsize='small')
# plt.xlabel(xlabel)
# plt.ylabel(ylabel)
# plt.title(title)
# plt.legend(bbox_to_anchor=(1.05,1.),loc=0,fontsize='xx-small')
# plt.yscale('log')
# plt.margins(y=0.2)
# plt.xlim([x_axis[0],x_axis[-1]])
# plt.tight_layout()
# plt.show()
main_ax.set_xticks(x_axis)
main_ax.set_xticklabels(layersets, rotation=90, fontsize='small')
main_ax.set_yscale('log')
main_ax.set_xlabel(xlabel)
main_ax.set_ylabel(ylabel)
main_ax.set_title(title)
#main_ax.legend(bbox_to_anchor=(1.05,0),loc='upper left',ncol=number_of_invariants,fontsize='small')
#main_ax.yscale('log')
main_ax.margins(y=0.2)
main_ax.set_xlim([x_axis[0], x_axis[-1]])
plt.tight_layout()
if savename == None:
plt.show()
else:
plt.savefig(savename, format='pdf')
def orbit_counts_all(net,
n,
nets,
invs,
auts,
orbit_list,
allowed_aspects='all'):
'''
Computes the orbit counts for all the nodes in net
Parameters
----------
net : network
n : int
max number of nodes
nets : dict (key: n_nodes, value: list of networks)
Graphlets, as produced by graphlets
invs : dict (key: str(complete invariant), value: tuple(n_nodes, net_index in nets))
complete invariants of the graphlets, as produced by graphlet
auts : dd (key: (n_nodes, net_index, node), value: node)
automorphisms, as produced by automorphism_orbits
orbit_list : list of orbits
as returned by ordered_orbit_list
allowed_aspects : list, string
the aspects that can be permutated when computing isomorphisms
Returns
-------
orbits : dd (key: (node, orbit), value: count)
Orbit counts for all the nodes
Notes
-----
Should be faster than orbit_counts if the counts are computed for all
(/ most of) the nodes
'''
nodes = net.slices[0]
layers = net.slices[1]
orbits = dd()
for node in nodes:
for orbit in orbit_list:
orbits[node, orbit] = 0
processed = set()
for node0 in nodes:
node_sets = set()
set_p = set([frozenset([node0])])
for _ in range(n - 1):
set_c = set()
for p in set_p:
for node_p in p:
for layer in layers:
node_o = net.__getitem__((node_p, layer))
for neighbor in node_o.iter_total():
if not (neighbor[0] in p
or neighbor[0] in processed):
set_n = frozenset(p | set([neighbor[0]]))
set_c.add(set_n)
node_sets = node_sets.union(set_c)
set_p = set_c.copy()
processed.add(node0)
for node_comb in node_sets:
sub_net = pymnet.subnet(net, node_comb, layers)
ci_sub = str(
pymnet.get_complete_invariant(sub_net,
allowed_aspects=allowed_aspects))
if ci_sub not in invs:
pymnet.draw(sub_net)
print(len(invs))
i = invs[ci_sub][0]
j = invs[ci_sub][1]
nw = nets[i][j]
iso = pymnet.get_isomorphism(sub_net,
nw,
allowed_aspects=allowed_aspects)
for node in node_comb:
if node in iso[0]:
orbits[node, (i, j, auts[i, j, iso[0][node]])] += 1
else:
orbits[node, (i, j, auts[i, j, node])] += 1
for layer in layers:
nls = list(net[node0, :, layer])
for node1 in nls:
net[node0, node1[0], layer] = 0 #remove edges
return orbits