Plotly for Python is now entirely open source, free, and self-hosted

Learn more about why we've open sourced

Show Sidebar Hide Sidebar

3D Network Graphs in Python

How to make 3D Network Graphs in Python.

3D Network Graphs with Plotly and igraph

A 3D graph representing the network of 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.

In [9]:
import igraph as ig

Read graph data from a json file:

In [10]:
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 [11]:
N=len(data['nodes'])
N
Out[11]:
77

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

In [12]:
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 [13]:
data['nodes'][0]
Out[13]:
{u'group': 1, u'name': u'Myriel'}
In [14]:
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 [15]:
layt=G.layout('kk', dim=3)

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

In [16]:
layt[5]
Out[16]:
[-2.419184216272965, -5.200101033772013, 4.673402139645248]

Set data for the Plotly plot of the graph:

In [17]:
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 [18]:
import plotly.plotly as py
from plotly.graph_objs import *
In [19]:
trace1=Scatter3d(x=Xe,
               y=Ye,
               z=Ze,
               mode='lines',
               line=Line(color='rgb(125,125,125)', width=1),
               hoverinfo='none'
               )
trace2=Scatter3d(x=Xn,
               y=Yn,
               z=Zn,
               mode='markers',
               name='actors',
               marker=Marker(symbol='dot',
                             size=6,
                             color=group,
                             colorscale='Viridis',
                             line=Line(color='rgb(50,50,50)', width=0.5)
                             ),
               text=labels,
               hoverinfo='text'
               )
In [20]:
axis=dict(showbackground=False,
          showline=False,
          zeroline=False,
          showgrid=False,
          showticklabels=False,
          title=''
          )
In [21]:
layout = Layout(
         title="Network of coappearances of characters in Victor Hugo's novel<br> Les Miserables (3D visualization)",
         width=1000,
         height=1000,
         showlegend=False,
         scene=Scene(
         xaxis=XAxis(axis),
         yaxis=YAxis(axis),
         zaxis=ZAxis(axis),
        ),
     margin=Margin(
        t=100
    ),
    hovermode='closest',
    annotations=Annotations([
           Annotation(
           showarrow=False,
            text="Data source: <a href='http://bost.ocks.org/mike/miserables/miserables.json'>[1]</a>",
            xref='paper',
            yref='paper',
            x=0,
            y=0.1,
            xanchor='left',
            yanchor='bottom',
            font=Font(
            size=14
            )
            )
        ]),    )
In [22]:
data=Data([trace1, trace2])
fig=Figure(data=data, layout=layout)

py.iplot(fig, filename='Les-Miserables')
Out[22]:
Still need help?
Contact Us

For guaranteed 24 hour response turnarounds, upgrade to our Premium or Enterprise plans.