Dolphin Society Networks in Doubtful Sound, NZ, part 2

Earlier, I posted an entry on dolphin society networks and some simple network drawings you can do with just NetworkX. Nowadays of course a lot of new fancy visualizations are available when you interface NetworkX with more modern plotting libraries, so we'll be taking a look at a few in the next parts of this series. Today's is 2-D plotting in plotly, and much of the code here comes from plotly's own well-written docs.

import pandas as pd

%pylab inline

Populating the interactive namespace from numpy and matplotlib

import networkx as nx
import numpy as np

We'll use the gml file written by NetworkX in Part 1.

g = nx.read_gml("dolphins.gml")

g

<networkx.classes.graph.Graph at 0x1a2500d208>

2-D plotting in plotly

2-D plotting in plotly involves defining a node trace, and an edge trace to let plotly know where the nodes should go in x,y space.

import plotly.graph_objs as go

import plotly.plotly as py

We set a node attribute, "pos", as the positions the nodes would take in a circular layout.

pos = nx.circular_layout(g)
nx.set_node_attributes(g, pos, 'pos')
#nx.get_node_attributes(g, "pos")

Here we use the plotly graph_objs.Scatter object to create a node_trace object, setting the sizes and colors of the nodes.

node_trace = go.Scatter(
    x=[],
    y=[],
    text=[],
    mode='markers',
    hoverinfo='text',
    marker=dict(
        showscale=True,
        # colorscale options
        #'Greys' | 'YlGnBu' | 'Greens' | 'YlOrRd' | 'Bluered' | 'RdBu' |
        #'Reds' | 'Blues' | 'Picnic' | 'Rainbow' | 'Portland' | 'Jet' |
        #'Hot' | 'Blackbody' | 'Earth' | 'Electric' | 'Viridis' |
        colorscale='YlGnBu',
        reversescale=True,
        color=[],
        size=10,
        colorbar=dict(
            thickness=15,
            title='Node Connections',
            xanchor='left',
            titleside='right'
        ),
        line=dict(width=2)))

We set the edge traces.

edge_trace = go.Scatter(
    x=[],
    y=[],
    line=dict(width=0.5,color='#888'),
    hoverinfo='none',
    mode='lines')

for edge in g.edges():
    x0, y0 = g.node[edge[0]]['pos']
    x1, y1 = g.node[edge[1]]['pos']
    edge_trace['x'] += tuple([x0, x1, None])
    edge_trace['y'] += tuple([y0, y1, None])

for node in g.nodes():
    x, y = g.node[node]['pos']
    node_trace['x'] += tuple([x])
    node_trace['y'] += tuple([y])

for node, adjacencies in enumerate(g.adjacency()):
    node_trace['marker']['color']+=tuple([len(adjacencies[1])])
    node_info = '# of connections: '+str(len(adjacencies[1]))
    node_trace['text']+=tuple([node_info])

import plotly

Plotly requires an API key for most applications so that is provided in the cell below; if you'd like to rerun this notebook, you would need to supply your own API key.

plotly.tools.set_credentials_file(username="user", api_key="")

fig = go.Figure(data=[edge_trace, node_trace],
             layout=go.Layout(
                title='<br>Network graph made with Python',
                titlefont=dict(size=16),
                showlegend=False,
                hovermode='closest',
                margin=dict(b=20,l=5,r=5,t=40),
                annotations=[ dict(
                    text="Python code: <a href='https://plot.ly/ipython-notebooks/network-graphs/'> https://plot.ly/ipython-notebooks/network-graphs/</a>",
                    showarrow=False,
                    xref="paper", yref="paper",
                    x=0.005, y=-0.002 ) ],
                xaxis=dict(showgrid=False, zeroline=False, showticklabels=False),
                yaxis=dict(showgrid=False, zeroline=False, showticklabels=False)))

py.iplot(fig, filename='networkx')

/Users/gbang/anaconda3/lib/python3.6/site-packages/IPython/core/display.py:689: UserWarning:

Consider using IPython.display.IFrame instead