Network Visualization

Overview of Visualization Techniques¶

The practice of visualizing networks is a subset of the larger field of information visualization. As the authors of The Network Turn describe, network visualization and quantitative network analysis were developed as distinct approaches around the same time, and each approach informs the other. It’s difficult to make quantitative arguments about networks without visualizations, and it’s difficult to make visual arguments about networks without quantification. Here is a short guide to creating effective network visualizations.

Visualization Resources¶

Gephi: A tool for static network visualization that also allows you to calculate metrics and work with many different layouts.
Network Navigator: A drag-and-drop web tool for network metrics and visualization.
Palladio: A drag-and-drop tool for data management and dynamic network visualization.
D3 Network Tutorial: A tutorial for using the D3.js JavaScript library to create dynamic network visualizations.
Graphology Tutorial: A tutorial for using the Graphology JavaScript library to create dynamic visualizations.

Static Visualization¶

Static network visualizations don’t respond to the viewer’s inputs, and they are typically single image files. They can be exploratory or explanatory, but in this class we will focus on creating explanatory visualizations that create a clear argument about a network. Here’s an example:

An example visualization of the Game of Thrones network.

This visualization uses the Game of Thrones network to make an argument about characters who co-occur in the A Song of Ice and Fire novels (on which the Game of Thrones TV series is based). The visualization uses clear labels, a readable layout, and a title, caption, and key to clearly communicate its argument. Rather than trying to show all aspects of the network, the visualization focuses in on just one thing. In static visualization, you may need to create more than one visualization if you have multiple aspects of the network you want to highlight.

You can visually adjust many different parts of a network to make a compelling visualization. Here’s a list of some of the possibilities:

Layout: The relative positions of nodes and edges can tell you a lot about the network and its parts. You can use a tabular or matrix layout to visualize a network without nodes and links. If you are using a classic node-link diagram like the one above, you can use irregular, regular, circular, rectilinear, or parallel layouts, and each one has different uses and highlights different things. In tools like Gephi, you also have access to a number of algorithmic layouts. We’ll discuss all of these layout possibilities in class.
Nodes: You can adjust node size to show a numerical value, node color to show a categorical or numerical value (using hue or brightness, respectively), and node position to indicate hierarchy, community, or change over time.
Edges: You can adjust edge thickness to show a numerical value, edge color to show a categorical or numerical value, and edge arrows or curve to show direction.
Labels: You can add labels to some or all of your nodes and edges to clearly indicate parts of your network. You can also use size and color with node labels in the same way you would use size and color of nodes. Sometimes, a network is most readable when you remove node circles entirely and use only labels.
Filters: It’s not always desirable to show the entire network. Some networks are very large and complex, and it might be helpful to filter down to a subset of nodes and edges in order to make an argument.

Dynamic Visualization¶

Dynamic visualization responds to the viewer’s inputs. In dynamic visualizations, you can click on things, move nodes around, and get more information about the network in various ways. All the principles of static visualization described above also apply to dynamic visualization. But because you can more easily show node movement and create new arrangements in a dynamic visualization, you can typically include a lot more information in a single visualization. The key to a dynamic visualization is that it allows someone to explore the network on their own. This makes it both easier and harder to communicate an argument with a dynamic visualization. There are more tools at your disposal, but the viewer also has considerable freedom.

Visualizing Networks with Python¶

While Gephi is a fine-grained tool for creating explanatory visualizations, you’ll often find a need for creating visualizations directly in your Python workflow, for either explanatory or exploratory purposes. NetworkX includes a robust interface for visualizing networks with matplotlib.

However, even their documentation recommends that for presentation-ready visualizations you’re best off exporting your data to a tool like Gephi. A visualization in Python is mainly useful as an intermediate step, or in instance where you’re visualizing something computationally complex (such as needing to create 10 or 20 iterations of the same visualization very quickly).

Using `draw()` and `display()`¶

NetworkX has a detailed API for drawing graphs using the draw() and draw_networkx() functions. While these functions are useful for fine-grained work, they require a lot of additional code since each visual element needs to be coded and added as a separate parameter.

Alternatively the newer display() function allows you to use Graph attributes to control what the final visualization looks like. You can use the built-in Karate Club graph as an example.

# Necessary libraries
import networkx as nx

# Read Karate Club data as example
G = nx.karate_club_graph()
print(G)

Graph named "Zachary's Karate Club" with 34 nodes and 78 edges

If called in its most basic form, the display function will try its best to create a readable visualization.

nx.display(G)

<networkx.classes.graph.Graph at 0x1133fb6b0>

You can customize the visualization by adding specific attributes to your Graph object. The documentation for display() outlines which attributes can be updated and what they can control. For instance, adding a 'size' attribute will determine the size of the nodes, and a 'width' attribute will determine the width of the edges. Here is some code that updates some specific attributes for visualization:

# Create a size variable by scaling up the degree centrality of nodes
# You copuld do this with any kind of centrality
degree = nx.degree_centrality(G)
size = {k:v*2000 for k,v in degree.items()}

# Run louvain community detection
# Create louvain variable from resulting communities to use as node color
from networkx.algorithms.community import louvain_communities
louvain = louvain_communities(G, seed=42)
louvain = {g:i for i,group in enumerate(louvain) for g in group}

# Create a pos (position) variable and use store_pos_as to create a "pos" attribute
pos = nx.spring_layout(G, store_pos_as="pos")

# Add all attributes to graph
# Add size attribute to graph directly
nx.set_node_attributes(G, size, 'size')
# Add louvain attribute to graph and use apply_matplotlib_colors to
# convert the group to a matplotlib "color" attribute
nx.set_node_attributes(G, louvain, "louvain")
nx.apply_matplotlib_colors(G, "louvain", "color", "tab10")

Running display() again after adding these attributes will alter the appearance of the visualization.

nx.display(G)

<networkx.classes.graph.Graph at 0x10a62ec90>

Instead of setting the default attributes, you can also tell display() which attributes to use by setting parameters within the display function. The following code will use the attributes you set above as well as some additional parameters.

nx.display(G, 
           node_label=False, # Turn off the node labels, which are the names of the nodes by default
           node_border_color="black", # Set node border to a specific color
           edge_width="weight" # Set edge width to the "weight" edge attribute
          )