from py2cytoscape.data.cynetwork import CyNetwork
from py2cytoscape.data.cyrest_client import CyRestClient
from py2cytoscape.data.style import StyleUtil
import py2cytoscape.util.cytoscapejs as cyjs
import py2cytoscape.cytoscapejs as renderer
import networkx as nx
import pandas as pd
import json
import igraph as ig
import rpy2.robjects.packages as rpackages
--------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-1-ed5dda1dbc56> in <module>() 11 import igraph as ig 12 ---> 13 import rpy2.robjects.packages as rpackages ImportError: No module named rpy2.robjects.packages
NUM_NODES = 100
g1 = ig.Graph.Barabasi(NUM_NODES, 2)
g2 = ig.Graph.GRG(NUM_NODES, 0.2)
cy = CyRestClient()
cy.network.create_from_igraph(g1)
cy.network.create_from_igraph(g2)
<py2cytoscape.data.cynetwork.CyNetwork at 0x10b80dd50>
g2.vs['label'] = [-1]*NUM_NODES
fix = [False]*NUM_NODES
node0 = g2.vs[40]
node1 = g2.vs[57]
ne1= node0.neighbors()
ne2= node1.neighbors()
print(ne1)
g2.vs[40]['label'] = 1
g2.vs[57]['label'] = 1
for n in ne1:
print(n.index)
g2.vs[n.index]['label'] = 1
for n in ne2:
print(n.index)
g2.vs[n.index]['label'] = 1
fix[40] = True
fix[57] = True
[igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,27,{'y': 0.4122450976155393, 'x': 0.26689583205779077, 'label': -1, 'community': 0, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,37,{'y': 0.4413342902926116, 'x': 0.4042221456555569, 'label': -1, 'community': 1, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,42,{'y': 0.3919489906377719, 'x': 0.4447844056662684, 'label': -1, 'community': 1, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,43,{'y': 0.4770437889078536, 'x': 0.4455614569474644, 'label': -1, 'community': 1, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,44,{'y': 0.7063847186804972, 'x': 0.4719754150531076, 'label': -1, 'community': 0, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,46,{'y': 0.4894698809295054, 'x': 0.48049028523140314, 'label': -1, 'community': 1, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,48,{'y': 0.4316934429074447, 'x': 0.48068638848412193, 'label': -1, 'community': 1, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,54,{'y': 0.5463835210708057, 'x': 0.5826852935480062, 'label': -1, 'community': 0, 'f1': None}), igraph.Vertex(<igraph.Graph object at 0x10a739ed8>,55,{'y': 0.4600141507637713, 'x': 0.5841189250955006, 'label': -1, 'community': 1, 'f1': None})] 27 37 42 43 44 46 48 54 55 39 47 50 59 64 67 69
res = g2.community_label_propagation(initial='label')
g2.vs['community'] = res.membership
cy.network.create_from_igraph(g2)
<py2cytoscape.data.cynetwork.CyNetwork at 0x10b981410>
yhq = pd.read_csv('/Applications/Cytoscape_v3.2.1/sampleData/yeastHighQuality.sif', sep=' ', names=['s', 'itr', 't'])
yhq = yhq.drop('itr', 1)
yhq.head()
yhq.to_csv('yhq.el', sep=' ')
ig.Graph.Read_Edgelist('yhq.el')
--------------------------------------------------------------------------- InternalError Traceback (most recent call last) <ipython-input-168-127fd4c64011> in <module>() ----> 1 ig.Graph.Read_Edgelist('yhq.el') InternalError: Error at foreign.c:101: parsing edgelist file failed, Parse error