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3D Network Graphs in Python/v3

How to make 3D Network Graphs in Python.


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Network reflecting coappearances of characters in
Victor Hugo's novel Les Miserables

We define our graph as an igraph.Graph object. Python igraph is a library for high-performance graph generation and analysis. Install the Python library with sudo pip install python-igraph.

In [1]:
import igraph as ig

Read graph data from a json file:

In [2]:
import json
import urllib2

data = []
req = urllib2.Request("https://raw.githubusercontent.com/plotly/datasets/master/miserables.json")
opener = urllib2.build_opener()
f = opener.open(req)
data = json.loads(f.read())

print data.keys()

[u'nodes', u'links']

Get the number of nodes:

In [3]:
N=len(data['nodes'])
N
Out[3]:
77

Define the list of edges and the Graph object from Edges:

In [4]:
L=len(data['links'])
Edges=[(data['links'][k]['source'], data['links'][k]['target']) for k in range(L)]

G=ig.Graph(Edges, directed=False)

Extract the node attributes, 'group', and 'name':

In [5]:
data['nodes'][0]
Out[5]:
{u'group': 1, u'name': u'Myriel'}
In [6]:
labels=[]
group=[]
for node in data['nodes']:
    labels.append(node['name'])
    group.append(node['group'])

Get the node positions, set by the Kamada-Kawai layout for 3D graphs:

In [7]:
layt=G.layout('kk', dim=3)

layt is a list of three elements lists (the coordinates of nodes):

In [8]:
layt[5]
Out[8]:
[4.195949332184983, 1.172321178571202, -2.5543268281789135]

Set data for the Plotly plot of the graph:

In [9]:
Xn=[layt[k][0] for k in range(N)]# x-coordinates of nodes
Yn=[layt[k][1] for k in range(N)]# y-coordinates
Zn=[layt[k][2] for k in range(N)]# z-coordinates
Xe=[]
Ye=[]
Ze=[]
for e in Edges:
    Xe+=[layt[e[0]][0],layt[e[1]][0], None]# x-coordinates of edge ends
    Ye+=[layt[e[0]][1],layt[e[1]][1], None]
    Ze+=[layt[e[0]][2],layt[e[1]][2], None]
In [10]:
import plotly.plotly as py
import plotly.graph_objs as go

trace1=go.Scatter3d(x=Xe,
               y=Ye,
               z=Ze,
               mode='lines',
               line=dict(color='rgb(125,125,125)', width=1),
               hoverinfo='none'
               )

trace2=go.Scatter3d(x=Xn,
               y=Yn,
               z=Zn,
               mode='markers',
               name='actors',
               marker=dict(symbol='circle',
                             size=6,
                             color=group,
                             colorscale='Viridis',
                             line=dict(color='rgb(50,50,50)', width=0.5)
                             ),
               text=labels,
               hoverinfo='text'
               )

axis=dict(showbackground=False,
          showline=False,
          zeroline=False,
          showgrid=False,
          showticklabels=False,
          title=''
          )

layout = go.Layout(
         title="Network of coappearances of characters in Victor Hugo's novel<br> Les Miserables (3D visualization)",
         width=1000,
         height=1000,
         showlegend=False,
         scene=dict(
             xaxis=dict(axis),
             yaxis=dict(axis),
             zaxis=dict(axis),
        ),
     margin=dict(
        t=100
    ),
    hovermode='closest',
    annotations=[
           dict(
           showarrow=False,
            text="Data source: <a href='http://bost.ocks.org/mike/miserables/miserables.json'>[1] miserables.json</a>",
            xref='paper',
            yref='paper',
            x=0,
            y=0.1,
            xanchor='left',
            yanchor='bottom',
            font=dict(
            size=14
            )
            )
        ],    )
In [11]:
data=[trace1, trace2]
fig=go.Figure(data=data, layout=layout)

py.iplot(fig, filename='Les-Miserables')
Out[11]:

Reference

See https://plotly.com/python/reference/#scatter3d for more information and chart attribute options!