def test_k_corona(self):
# k=0
k_corona_subgraph = nx.k_corona(self.H, k=2)
assert_equal(sorted(k_corona_subgraph.nodes()), [2, 4, 5, 6])
# k=1
k_corona_subgraph = nx.k_corona(self.H, k=1)
assert_equal(sorted(k_corona_subgraph.nodes()), [1])
# k=2
k_corona_subgraph = nx.k_corona(self.H, k=0)
assert_equal(sorted(k_corona_subgraph.nodes()), [0])
def test_k_corona(self):
# k=0
k_corona_subgraph = nx.k_corona(self.H, k=2)
assert_equal(sorted(k_corona_subgraph.nodes()), [2, 4, 5, 6])
# k=1
k_corona_subgraph = nx.k_corona(self.H, k=1)
assert_equal(sorted(k_corona_subgraph.nodes()), [1])
# k=2
k_corona_subgraph = nx.k_corona(self.H, k=0)
assert_equal(sorted(k_corona_subgraph.nodes()), [0])
def test_k_corona(self):
# k=0
k_corona_subgraph = nx.k_corona(self.H, k=2)
assert sorted(k_corona_subgraph.nodes()) == [2, 4, 5, 6]
# k=1
k_corona_subgraph = nx.k_corona(self.H, k=1)
assert sorted(k_corona_subgraph.nodes()) == [1]
# k=2
k_corona_subgraph = nx.k_corona(self.H, k=0)
assert sorted(k_corona_subgraph.nodes()) == [0]
def generate_graph_features(glycan, libr=None):
"""compute graph features of glycan\n
| Arguments:
| :-
| glycan (string): glycan in IUPAC-condensed format
| libr (list): library of monosaccharides; if you have one use it, otherwise a comprehensive lib will be used\n
| Returns:
| :-
| Returns a pandas dataframe with different graph features as columns and glycan as row
"""
if libr is None:
libr = lib
g = glycan_to_nxGraph(glycan, libr=libr)
#nbr of different node features:
nbr_node_types = len(set(nx.get_node_attributes(g, "labels")))
#adjacency matrix:
A = nx.to_numpy_matrix(g)
N = A.shape[0]
diameter = nx.algorithms.distance_measures.diameter(g)
deg = np.array([np.sum(A[i, :]) for i in range(N)])
dens = np.sum(deg) / 2
avgDeg = np.mean(deg)
varDeg = np.var(deg)
maxDeg = np.max(deg)
nbrDeg4 = np.sum(deg > 3)
branching = np.sum(deg > 2)
nbrLeaves = np.sum(deg == 1)
deg_to_leaves = np.array([np.sum(A[:, deg == 1]) for i in range(N)])
max_deg_leaves = np.max(deg_to_leaves)
mean_deg_leaves = np.mean(deg_to_leaves)
deg_assort = nx.degree_assortativity_coefficient(g)
betweeness_centr = np.array(
pd.DataFrame(nx.betweenness_centrality(g), index=[0]).iloc[0, :])
betweeness = np.mean(betweeness_centr)
betwVar = np.var(betweeness_centr)
betwMax = np.max(betweeness_centr)
betwMin = np.min(betweeness_centr)
eigen = np.array(
pd.DataFrame(nx.katz_centrality_numpy(g), index=[0]).iloc[0, :])
eigenMax = np.max(eigen)
eigenMin = np.min(eigen)
eigenAvg = np.mean(eigen)
eigenVar = np.var(eigen)
close = np.array(
pd.DataFrame(nx.closeness_centrality(g), index=[0]).iloc[0, :])
closeMax = np.max(close)
closeMin = np.min(close)
closeAvg = np.mean(close)
closeVar = np.var(close)
flow = np.array(
pd.DataFrame(nx.current_flow_betweenness_centrality(g),
index=[0]).iloc[0, :])
flowMax = np.max(flow)
flowMin = np.min(flow)
flowAvg = np.mean(flow)
flowVar = np.var(flow)
flow_edge = np.array(
pd.DataFrame(nx.edge_current_flow_betweenness_centrality(g),
index=[0]).iloc[0, :])
flow_edgeMax = np.max(flow_edge)
flow_edgeMin = np.min(flow_edge)
flow_edgeAvg = np.mean(flow_edge)
flow_edgeVar = np.var(flow_edge)
load = np.array(pd.DataFrame(nx.load_centrality(g), index=[0]).iloc[0, :])
loadMax = np.max(load)
loadMin = np.min(load)
loadAvg = np.mean(load)
loadVar = np.var(load)
harm = np.array(
pd.DataFrame(nx.harmonic_centrality(g), index=[0]).iloc[0, :])
harmMax = np.max(harm)
harmMin = np.min(harm)
harmAvg = np.mean(harm)
harmVar = np.var(harm)
secorder = np.array(
pd.DataFrame(nx.second_order_centrality(g), index=[0]).iloc[0, :])
secorderMax = np.max(secorder)
secorderMin = np.min(secorder)
secorderAvg = np.mean(secorder)
secorderVar = np.var(secorder)
x = np.array([len(nx.k_corona(g, k).nodes()) for k in range(N)])
size_corona = x[x > 0][-1]
k_corona = np.where(x == x[x > 0][-1])[0][-1]
x = np.array([len(nx.k_core(g, k).nodes()) for k in range(N)])
size_core = x[x > 0][-1]
k_core = np.where(x == x[x > 0][-1])[0][-1]
M = ((A + np.diag(np.ones(N))).T / (deg + 1)).T
eigval, vec = eigsh(M, 2, which='LM')
egap = 1 - eigval[0]
distr = np.abs(vec[:, -1])
distr = distr / sum(distr)
entropyStation = np.sum(distr * np.log(distr))
features = np.array([
diameter, branching, nbrLeaves, avgDeg, varDeg, maxDeg, nbrDeg4,
max_deg_leaves, mean_deg_leaves, deg_assort, betweeness, betwVar,
betwMax, eigenMax, eigenMin, eigenAvg, eigenVar, closeMax, closeMin,
closeAvg, closeVar, flowMax, flowAvg, flowVar, flow_edgeMax,
flow_edgeMin, flow_edgeAvg, flow_edgeVar, loadMax, loadAvg, loadVar,
harmMax, harmMin, harmAvg, harmVar, secorderMax, secorderMin,
secorderAvg, secorderVar, size_corona, size_core, nbr_node_types, egap,
entropyStation, N, dens
])
col_names = [
'diameter', 'branching', 'nbrLeaves', 'avgDeg', 'varDeg', 'maxDeg',
'nbrDeg4', 'max_deg_leaves', 'mean_deg_leaves', 'deg_assort',
'betweeness', 'betwVar', 'betwMax', 'eigenMax', 'eigenMin', 'eigenAvg',
'eigenVar', 'closeMax', 'closeMin', 'closeAvg', 'closeVar', 'flowMax',
'flowAvg', 'flowVar', 'flow_edgeMax', 'flow_edgeMin', 'flow_edgeAvg',
'flow_edgeVar', 'loadMax', 'loadAvg', 'loadVar', 'harmMax', 'harmMin',
'harmAvg', 'harmVar', 'secorderMax', 'secorderMin', 'secorderAvg',
'secorderVar', 'size_corona', 'size_core', 'nbr_node_types', 'egap',
'entropyStation', 'N', 'dens'
]
feat_dic = {col_names[k]: features[k] for k in range(len(features))}
return pd.DataFrame(feat_dic, index=[glycan])
nx.draw_networkx(F, pos, **dzcnapy.attrs)
dzcnapy.set_extent(pos, plt)
dzcnapy.plot("abcNwtwork")
G = nx.Graph(
(("Alpha", "Bravo"), ("Bravo", "Charlie"), ("Charlie", "Delta"),
("Charlie", "Echo"), ("Charlie", "Foxtrot"), ("Delta", "Echo"),
("Delta", "Foxtrot"), ("Echo", "Foxtrot"), ("Echo", "Golf"),
("Echo", "Hotel"), ("Foxtrot", "Golf"), ("Foxtrot", "Hotel"),
("Delta", "Hotel"), ("Golf", "Hotel"), ("Delta", "India"),
("Charlie", "India"), ("India", "Juliet"), ("Golf", "Kilo"),
("Alpha", "Kilo"), ("Bravo", "Lima")))
pos = graphviz_layout(G)
core = nx.k_core(G)
crust = nx.k_crust(G)
corona3 = nx.k_corona(G, k=3).nodes()
nx.draw_networkx(G, pos, nodelist=core, **dzcnapy.attrs)
nx.draw_networkx_edges(G, pos, core.edges(), **dzcnapy.tick_attrs)
nx.draw_networkx_edges(G, pos, crust.edges(), **dzcnapy.tick_attrs)
nx.draw_networkx_nodes(G, pos, crust, node_shape='v', **dzcnapy.attrs)
nx.draw_networkx_nodes(G, pos, corona3, node_shape='s', **dzcnapy.attrs)
dzcnapy.set_extent(pos, plt)
dzcnapy.plot("CoresAndCoronas")
# Generate a 5-clique
G = nx.complete_graph(5, nx.Graph())
nx.relabel_nodes(G, dict(enumerate(("Alpha", "Bravo", "Charlie", "Delta", "Echo"))),
copy=False)
# Attach a pigtail to it
G.add_edges_from([("Echo", "Foxtrot"), ("Foxtrot", "Golf"), ("Foxtrot", "Hotel"),
def main():
#Reading in the graph
G = nx.read_edgelist("GameOfThrones.txt",
delimiter=",",
data=(('strength', int), ('season', int)))
#Displaying the graph
pos = nx.spring_layout(G)
plt.figure(figsize=(10, 10))
nx.draw_networkx(G, pos=pos, with_labels=True)
plt.axis('off')
plt.show()
#Outputting info
print(nx.info(G))
#Outputting highest degree node name & degree
nodes = list(G.degree())
print("\nHighest degree node is:", nodes[0][0], "with degree", nodes[0][1])
#Outputting num of connected components
print("\nNumber of connected components:",
len(list(nx.connected_components(G))))
#Outputting the num of maximal cliques
print("\nNumber of maximal cliques:", len(list(nx.find_cliques(G))))
#Outputting num of nodes in main core and k val
core_num = list(nx.k_core(G).nodes())
for x in range(len(core_num)):
if core_num == list(nx.k_core(G, k=x)):
k_val = x
print("\nNumber of nodes in main core:", len(core_num), "with k val:",
k_val)
#Outputting num of nodes in main crust
print("\nNumber of nodes in main crust:", len(list(nx.k_crust(G).nodes())))
#Output num of nodes in the k corona
print("\nNumber of nodes in k corona:",
len(list(nx.k_corona(G, k=k_val).nodes())))
#Output num of nodes in main shell
print("\nNumber of nodes in main shell:", len(list(nx.k_shell(G).nodes())))
#Display graph, main core - red, main crust - blue
color_map = []
for node in G:
if node in list(nx.k_core(G).nodes()):
color_map.append('red')
elif node in list(nx.k_crust(G).nodes()):
color_map.append('blue')
nx.draw_networkx(G, pos=pos, node_color=color_map, with_labels=False)
plt.axis('off')
plt.show()
#Louvain Method, output num of communities, size or largest commnunity, size of smallest community, modularity of partition
partition = community.best_partition(G)
com_num = partition[max(partition, key=partition.get)]
print("\nLouvain Method:")
print("Number of communities:", com_num + 1)
count = []
comm_list = list(partition.values())
for x in range(com_num):
count.append(comm_list.count(x))
print("The largest community has count:", max(count))
print("The smallest community has count:", min(count))
print("The modularity of this partitioning:",
community.modularity(partition, G))
#Display graph using Louvain, with nodes in diff colors per partition
cmap = cm.get_cmap('viridis', max(partition.values()) + 1)
nx.draw_networkx_nodes(G,
pos,
partition.keys(),
node_size=40,
cmap=cmap,
node_color=list(partition.values()))
nx.draw_networkx_edges(G, pos, alpha=0.5)
plt.axis('off')
plt.show()
#Girvan-Newman Method, output num of communities, size or largest commnunity, size of smallest community, modularity of partition
print("\nGirvan-Newman Method:")
components = c.girvan_newman(G)
i = 0
for row in components:
if (i == 0):
finalResult = row
i = i + 1
partitions = dict()
L = list(finalResult)
p = 0
for comp in L:
for entry in comp:
partitions[entry] = p
p = p + 1
com_num = partitions[max(partitions, key=partitions.get)]
print("Number of communities:", com_num + 1)
count = []
comm_list = list(partition.values())
for x in range(com_num):
count.append(comm_list.count(x))
print("The largest community has count:", max(count))
print("The smallest community has count:", min(count))
print("The modularity of this partitioning:",
community.modularity(partitions, G))
#Display graph using Girvan-Newman, with nodes in diff colors per partition
cmap = cm.get_cmap('viridis', max(partitions.values()) + 1)
nx.draw_networkx_nodes(G,
pos,
partitions.keys(),
node_size=60,
cmap=cmap,
node_color=list(partitions.values()))
plt.axis('off')
plt.show()
ig.plot(g,
target=fig_name,
layout=layout,
vertex_size=7,
vertex_color='gray',
vertex_label_size=10,
vertex_label_dist=2,
mark_groups=group_markers) #vertex_label=None
print 'Ορισμός: Το k-στέμμα είναι ο υπογράφος των κόμβων του k-πυρήνα, οι οποίοι κόμβοι έχουν ακριβώς k γείτονες στον k-πυρήνα.'
# print 'DEFINITION: The k-corona is the subgraph of nodes in the k-core which have exactly k neighbours in the k-core. στέμμα'
print str(" ")
kcoronas = []
for i in set(nx.core_number(G).values()):
if len(nx.k_corona(G, k=i).nodes()) > 0:
# print "i =", i
kcnGi = nx.k_corona(G, k=i)
print 'Οι κόμβοι του', str(i) + '-στέμματος:'
# print 'The nodes of the', str(i)+'-shell:'
print kcnGi.nodes()
# print 'Οι ακμές του', str(i)+'-στέμματος:'
# # print 'The edges of the k-shell of G are:'
# print kcnGi.edges()
# print 'Η ακολουθία βαθμών των κόμβων του', str(i)+'-στέμματος:'
# # print 'The degree sequence of the nodes of the', str(i)+'-shell:'
# print list(nx.degree(ksGi).values())
# # # print 'The order of the main k-shell of G is:'
# # # print 'k =', min(list(nx.degree(ksGi).values()))
print str(" ")
kcoronas.append(kcnGi.nodes())
import networkx as nx
import plot_multigraph
import matplotlib.pylab as plt
from matplotlib import pylab as plt
n = 80
k = int(.2 * n)
p = 10. / n
G = nx.fast_gnp_random_graph(n, p, seed=42)
def set_to_list(set_, G):
return [1. * (k in set_) for k in G.nodes()]
graph_colors = [
("center", set_to_list(nx.center(G), G)),
("periphery", set_to_list(nx.periphery(G), G)),
("k_core", set_to_list(nx.k_core(G), G)),
("k_shell", set_to_list(nx.k_shell(G), G)),
("k_crust", set_to_list(nx.k_crust(G), G)),
("k_corona", set_to_list(nx.k_corona(G, k), G)),
]
fig = plot_multigraph.plot_color_multigraph(G, graph_colors, 2, 3, node_size=50)
plt.savefig('graphs/sets.png', facecolor=fig.get_facecolor())
color_to_set=(random.random(),random.random(),1)
colors_lists.append(color_to_set)
group_markers = [(kcrusts[i], colors_lists[i]) for i in range(len(kcrusts))]
# ig.plot(g, mark_groups=group_markers)
fig_name=os.path.join(file_dir_figs,str(G.name)+'_[k='+str(max(nx.core_number(G).values()))+']_k-crusts.png')
ig.plot(g, target=fig_name, layout=layout, vertex_size=7, vertex_color='gray', vertex_label_size=10, vertex_label_dist=2, mark_groups=group_markers) #vertex_label=None
print 'Ορισμός: Το k-στέμμα είναι ο υπογράφος των κόμβων του k-πυρήνα, οι οποίοι κόμβοι έχουν ακριβώς k γείτονες στον k-πυρήνα.'
# print 'DEFINITION: The k-corona is the subgraph of nodes in the k-core which have exactly k neighbours in the k-core. στέμμα'
print str(" ")
kcoronas=[]
for i in set(nx.core_number(G).values()):
if len(nx.k_corona(G,k=i).nodes()) > 0:
# print "i =", i
kcnGi=nx.k_corona(G,k=i)
print 'Οι κόμβοι του', str(i)+'-στέμματος:'
# print 'The nodes of the', str(i)+'-shell:'
print kcnGi.nodes()
# print 'Οι ακμές του', str(i)+'-στέμματος:'
# # print 'The edges of the k-shell of G are:'
# print kcnGi.edges()
# print 'Η ακολουθία βαθμών των κόμβων του', str(i)+'-στέμματος:'
# # print 'The degree sequence of the nodes of the', str(i)+'-shell:'
# print list(nx.degree(ksGi).values())
# # # print 'The order of the main k-shell of G is:'
# # # print 'k =', min(list(nx.degree(ksGi).values()))
print str(" ")
kcoronas.append(kcnGi.nodes())
coreGraph.add_edge(edge[0], edge[1])
drawGraph(coreGraph)
'''
################################################
Step 4 output:
a) Number of nodes in the main crust
##################################################'''
print("\nNumber of nodes in the main crust: " +
str(len(nx.k_crust(G).nodes())))
'''
################################################
Step 5 output:
a) Number of nodes in the k-corona where k is the max k-val (main core kval)
##################################################'''
print("\nNumber of nodes in the k-corona: " +
str(len(nx.k_corona(G, k=maxKValue).nodes())))
coronaGraph = nx.Graph()
coronaEdges = nx.k_corona(G, k=maxKValue).edges()
for edge in coronaEdges():
coronaGraph.add_edge(edge[0], edge[1])
drawGraph(coronaGraph)
'''
################################################
Step 6 output:
a) Number of nodes in the main shell
##################################################'''
mainShell = nx.k_shell(G).nodes()
mainShellEdges = nx.k_shell(G).edges()
print("\nNumber of nodes in main shell: " + str(len(mainShell)))