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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]:

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!

In [1]:

from IPython.display import display, HTML

display(HTML('<link href="//fonts.googleapis.com/css?family=Open+Sans:600,400,300,200|Inconsolata|Ubuntu+Mono:400,700" rel="stylesheet" type="text/css" />'))
display(HTML('<link rel="stylesheet" type="text/css" href="http://help.plot.ly/documentation/all_static/css/ipython-notebook-custom.css">'))

! pip install git+https://github.com/plotly/publisher.git --upgrade

import publisher
publisher.publish(
    'Les-miserables-network.ipynb', 'python/3d-network-graph/', 'Python 3D Network Graphs',
    'How to make 3D Network Graphs in Python. ',
    title = '3D Network Graphs in Python | plotly',
    name = '3D Network Graphs',
    has_thumbnail='true', thumbnail='thumbnail/3dnetwork.jpg', 
    language='python', page_type='example_index', 
    display_as='3d_charts', order=13,
    ipynb= '~notebook_demo/226')

Collecting git+https://github.com/plotly/publisher.git
  Cloning https://github.com/plotly/publisher.git to c:\users\thars\appdata\local\temp\pip-req-build-ogrbpd
Building wheels for collected packages: publisher
  Running setup.py bdist_wheel for publisher: started
  Running setup.py bdist_wheel for publisher: finished with status 'done'
  Stored in directory: c:\users\thars\appdata\local\temp\pip-ephem-wheel-cache-unt43t\wheels\99\3e\a0\fbd22ba24cca72bdbaba53dbc23c1768755fb17b3af0f33966
Successfully built publisher
Installing collected packages: publisher
  Found existing installation: publisher 0.11
    Uninstalling publisher-0.11:
      Successfully uninstalled publisher-0.11
Successfully installed publisher-0.11

C:\Anaconda\Anaconda2\lib\site-packages\IPython\nbconvert.py:13: ShimWarning: The `IPython.nbconvert` package has been deprecated since IPython 4.0. You should import from nbconvert instead.
  "You should import from nbconvert instead.", ShimWarning)
C:\Anaconda\Anaconda2\lib\site-packages\publisher\publisher.py:53: UserWarning: Did you "Save" this notebook before running this command? Remember to save, always save.
  warnings.warn('Did you "Save" this notebook before running this command? '

In [ ]:

New to Plotly?¶

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

Reference¶

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