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Mastering Gephi Network Visualization
Mastering Gephi Network Visualization

Mastering Gephi Network Visualization: Produce advanced network graphs in Gephi and gain valuable insights into your network datasets

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Mastering Gephi Network Visualization

Chapter 2. A Network Graph Framework

As one embarks on the task of creating a network graph, it quickly becomes apparent that neither is there a shortage of topics to visualize, nor is there a lack of data detailing many potential sets of network relationships. The more difficult task is to determine what we choose to visualize and how to move from a simple idea to a finished graph. In this chapter, you will be exposed to a proposed framework that details how this author goes through the entire process from the initial idea to a final published graph. The chapter will then take you through an actual example, where we can begin creating a network graph together.

In the following sections, I will discuss my personal approach to create a finished graph using the following:

  • Identifying an idea or topic to pursue
  • Determining the final output
  • Identifying the data source(s) needed to populate the graph
  • Formatting the data for Gephi according to the required naming conventions
  • Importing data...

A proposed process flow

This process might seem like a lot of steps, but it is meant merely to provide a framework to move an idea from your imagination to a final published graph. In fact, you might find a better approach or might already be using a different workflow that suits your particular style or specific needs. By all means, if it works for you, keep using it. On the other hand, if you are new to this discipline and need some direction, then follow this process to get started. I have found that especially in cases where there are multiple graphs to be created around a common theme or dataset, this process can make graph creation more efficient to move from start to finish. So let's get started, and we can ultimately get to the best part—actually creating and publishing some graphs.

Identifying an idea or topic

The world around us is literally filled with examples of networks, ranging from our own social media connections through very complex webs of information, such...

Creating an example graph

Now that we've been through the process, it's time to have a little fun by following the preceding steps from start to finish using actual network data. Think of this as a bit of a case study where we put the theoretical process to work with a real dataset. The goal here is to get you acquainted with many of the capabilities within Gephi and to see how they might be used when you create your own graphs first hand.

So let's follow the process outlined earlier, walking through each step. Only this time, we're going to come up with an idea, retrieve the data for it, and create a network graph.

Identifying the topic

Choosing a topic for a network graph is not an easy task, given the hundreds of thousands of possibilities available to us, courtesy the Web and its numerous datasets. Even when a topic area is narrowed down to a specific genre (say, infrastructure networks), there are often multiple potential networks that could be created. Let's...

Analyzing the graph

Now that we have settled upon a layout, let's take some time to perform a cursory analysis of the network to see what patterns can be identified and begin understanding relationships within the network. In Chapter 4, Network Patterns, and Chapter 6, Graph Statistics, we'll venture much further into analyzing some graphs from both visual and technical perspectives, but let's get a head start on the process.

Here's the Yifan Hu layout we saw previously:

Analyzing the graph

The Yifan Hu layout

Let your eyes scan the graph for a few moments to understand more about the network. Ready? Here are a few things you might have noticed:

  • The graph is still somewhat difficult to navigate
  • A number of nodes have been forced away from the center and appear to have single edges in many cases
  • There are no obvious hubs (high degree nodes) to be seen
  • Several linear connections appear, with several nodes connected in sequence— although this is only evident when zooming into the graph

Now...

Modifying the graph

No network graph is ever perfect, no matter how much time one spends tweaking it, but every graph can be substantially improved from the original output, whether you are using Gephi or any other graph analysis tool. Even a well-selected algorithm using carefully prepared data is unlikely to provide the exact output we seek. This is why the final modifications, either manually applied or executed using some broad criteria (clusters, partitions, and so on), invariably add more power to the finished graph. Whether the modifications address aesthetic, technical, or navigational aspects of the network, these final tweaks will lead to a better output than that provided by total dependence on the data and the layout algorithm.

Recall our earlier selection of the Yifan Hu output for the power grid network display. While the network had improved considerably from its original version, there are still some simple actions that will make the network far more useful for viewers. Let...

Exporting the graph

Now we need to think back to the start of this process, when we were considering what our visualization was intended to do and how it would ultimately be used. For now, let's assume we don't want an interactive graph but simply a static network in two versions: one for quick display and another that can be modified for future use. Chapter 9, Taking Your Graph Beyond Gephi, will explore the interactive options in considerable detail as well as delve a bit further into the default static types.

There are two quick ways in which we can export a static version of the network graph. The first is to navigate to File | Export | SVG/PDF/PNG file, which will load a dialog window with some basic options available dependent on the export type selected. An alternative way to arrive at the same place is to use the SVG/PDF/PNG button available at the bottom of the Preview window.

The PNG option will create a simple graph image suitable for sharing through e-mail or social...

A proposed process flow


This process might seem like a lot of steps, but it is meant merely to provide a framework to move an idea from your imagination to a final published graph. In fact, you might find a better approach or might already be using a different workflow that suits your particular style or specific needs. By all means, if it works for you, keep using it. On the other hand, if you are new to this discipline and need some direction, then follow this process to get started. I have found that especially in cases where there are multiple graphs to be created around a common theme or dataset, this process can make graph creation more efficient to move from start to finish. So let's get started, and we can ultimately get to the best part—actually creating and publishing some graphs.

Identifying an idea or topic

The world around us is literally filled with examples of networks, ranging from our own social media connections through very complex webs of information, such as the connections...

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Description

This book is intended for anyone interested in advanced network analysis. If you wish to master the skills of analyzing and presenting network graphs effectively, then this is the book for you. No coding experience is required to use this book, although some familiarity with the Gephi user interface will be helpful.

Who is this book for?

This book is intended for anyone interested in advanced network analysis. If you wish to master the skills of analyzing and presenting network graphs effectively, then this is the book for you. No coding experience is required to use this book, although some familiarity with the Gephi user interface will be helpful.
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Publication date : Jan 28, 2015
Length: 378 pages
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Language : English
ISBN-13 : 9781783987344
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Table of Contents

12 Chapters
1. Fundamentals of Complex Networks and Gephi Chevron down icon Chevron up icon
2. A Network Graph Framework Chevron down icon Chevron up icon
3. Selecting the Layout Chevron down icon Chevron up icon
4. Network Patterns Chevron down icon Chevron up icon
5. Working with Filters Chevron down icon Chevron up icon
6. Graph Statistics Chevron down icon Chevron up icon
7. Segmenting and Partitioning a Graph Chevron down icon Chevron up icon
8. Dynamic Networks Chevron down icon Chevron up icon
9. Taking Your Graph Beyond Gephi Chevron down icon Chevron up icon
10. Putting It All Together Chevron down icon Chevron up icon
A. Data Sources and Other Web Resources Chevron down icon Chevron up icon
Index Chevron down icon Chevron up icon

Customer reviews

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Full star icon Full star icon Full star icon Full star icon Half star icon 4.6
(8 Ratings)
5 star 75%
4 star 12.5%
3 star 12.5%
2 star 0%
1 star 0%
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TM May 15, 2015
Full star icon Full star icon Full star icon Full star icon Full star icon 5
Mastering Gephi Network Visualization is a great get start guide for someone wanting learn how to create great graphs using Gephi. Helped me better understand how to visualize the statistics that mattered.
Amazon Verified review Amazon
Amazon Customer May 29, 2015
Full star icon Full star icon Full star icon Full star icon Full star icon 5
This book explains easily the best way to use Gehpi resources, managing file, reports, graphs, etc.
Amazon Verified review Amazon
Jean May 22, 2015
Full star icon Full star icon Full star icon Full star icon Full star icon 5
I struggled with Gephi for months. This book lays out everything you need to know to get started and then some. It's highly practical yet includes theory when needed. It does so in a natural and unobtrusive way. All functions are illustrated using publicly available datasets. It is written in a clear and easy to follow conversational manner. I couldn't ask for more.
Amazon Verified review Amazon
Steven P. Sanderson May 03, 2015
Full star icon Full star icon Full star icon Full star icon Full star icon 5
Mastering network visualization with Gephi was an excellent guide in creating graphs that are both informative and appealing. This book serves as an excellent framework of how to properly and effectively navigate Gephi and its abilities to create graphs. This book also allows you to understand the many intricacies of network visualization, what type of layout to use, what do the graph statistics tell you, what is going on. These are all questions that anyone trying to visualize data will have and it is not always obvious how to go about getting answers to them, this book makes answering those questions possible.
Amazon Verified review Amazon
Vyacheslav Jun 23, 2015
Full star icon Full star icon Full star icon Full star icon Full star icon 5
Huge improvement over previous Gephi title by same author. Many useful tips for all Gephi workflow stages.One downside for me - it is not clear how to contact author - no email in the book or on his blog. He uses Sigma.js export somehow differently (not as the book) in one his recent visualization with group filtering. I can't figure out how it was done, but this is very useful. I wish he shown this in the book in chapter dedicated to Sigma.js export.
Amazon Verified review Amazon
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