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  • Book Overview & Buying Gephi Cookbook
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Gephi Cookbook

Gephi Cookbook

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Gephi Cookbook

Gephi Cookbook

5 (1)
Buy this Book

Overview of this book

If you want to learn network analysis and visualization along with graph concepts from scratch, then this book is for you. This is ideal for those of you with little or no understanding of Gephi and this domain, but will also be beneficial for those interested in expanding their knowledge and experience.
Table of Contents (12 chapters)
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Preface
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Preface
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What this book covers
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What you need for this book
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Who this book is for
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Sections
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Conventions
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Reader feedback
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Customer support
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1
1. Getting Started with Gephi
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1. Getting Started with Gephi
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Introduction
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Installing Gephi
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Troubleshooting the Gephi installation
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Exploring Gephi's graphical user interface
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The basics of working in the Overview mode
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The basics of working in the Data Laboratory mode
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The basics of working in the Preview mode
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2. Basic Graph Manipulations
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2. Basic Graph Manipulations
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Introduction
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Generating a random graph
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Selecting and highlighting nodes in the graph
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Coloring and sizing nodes in the graph
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Adding nodes and edges to the graph
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Editing node attributes in the graph
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Finding out the shortest path in the graph
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Setting the edge and label properties
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Setting basic properties for graphs, nodes, edges, and labels
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Changing the background color of the graph
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Generating a heat map for the graph
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Showing convex hulls for a graph where a hierarchy exists
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Showing/hiding various parts of the graph
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Reverting changes in the graph to the original presets
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Creating a PNG file directly from the graph window in user-specified sizes
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3. Using Graph Layout Algorithms
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3. Using Graph Layout Algorithms
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Introduction
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Using the Clockwise Rotate layout algorithm
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Using the Counter-Clockwise Rotate layout algorithm
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Using the Contraction layout algorithm
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Using the Expansion layout algorithm
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Using the Force Atlas layout algorithm
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Using the Force Atlas 2 layout algorithm
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Using the Fruchterman Reingold layout algorithm
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Using the Label Adjust layout algorithm
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Using the Random Layout algorithm
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Using the Yifan Hu layout algorithm
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Using the Yifan Hu Proportional layout algorithm
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Using the Yifan Hu Multilevel layout algorithm
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4. Working with Partition and Ranking Algorithms
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4. Working with Partition and Ranking Algorithms
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Introduction
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Partitioning the graph based on node attributes
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Partitioning the graph based on edge attributes
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Configuring node colors in a graph by ranking nodes
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Configuring node sizes in a graph by ranking nodes
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Configuring node label colors in a graph by ranking nodes
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Configuring node label sizes in a graph by ranking nodes
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Configuring edge colors in a graph by ranking edges
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Configuring the colors of edge labels in a graph by ranking edges
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Configuring the size of edge labels in a graph by ranking edges
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5. Running Metrics, Filters, and Timelines
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5. Running Metrics, Filters, and Timelines
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Introduction
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Selecting a list of metrics for a graph
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Finding the average degree and average weighted degree of a graph
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Finding the network diameter
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Finding graph density
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Finding the HITS value for a graph
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Finding a graph's modularity
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Finding a graph's PageRank
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Finding connected components in a graph
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Getting a node overview of a graph
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Getting an edge overview of a graph
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Getting dynamic statistics for a graph
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Applying individual filters on a graph
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Applying a combination of filters on a graph
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Filtering dynamic graphs based on time intervals
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6. Working in the Data Laboratory Mode
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6. Working in the Data Laboratory Mode
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Introduction
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Importing a spreadsheet
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Adding and deleting nodes in a graph
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Changing the attributes of an existing node in a graph
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Adding and deleting edges in a graph
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Changing the attributes of an existing edge in a graph
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Adding/deleting columns
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Merging columns
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Copying data between columns
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Filtering, searching, and modifying data based on particular attributes
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Creating columns with dynamic regular expression filtering
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Exporting a table
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7. Getting Graphs and Networks Ready for Preview
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7. Getting Graphs and Networks Ready for Preview
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Introduction
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Previewing and fine-tuning a graph in the Default mode
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Previewing and fine-tuning a graph in the Default Curved mode
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Previewing and fine-tuning a graph in the Default Straight mode
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Previewing and fine-tuning a graph in the Text outline mode
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Previewing and fine-tuning a graph in the Black Background mode
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Previewing and fine-tuning a graph in the Edges Custom Color mode
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Previewing and fine-tuning a graph in the Tag Cloud mode
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Exporting a graph in the SVG, PNG, or PDF format
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8. Exploring Dynamic and Multilevel Graphs
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8. Exploring Dynamic and Multilevel Graphs
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Introduction
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Building dynamic/temporal graphs in Gephi
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Working with dynamic/temporal graphs
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Working with multilevel graphs
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Expanding and contracting subgraphs in metanodes
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Clustering links and attributes
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9. Getting Real-world Graph Datasets
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9. Getting Real-world Graph Datasets
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Introduction
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Exploring the Web and Internet domain – EuroSiS Web mapping study
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Exploring the Web and Internet domain – the Internet dataset
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Exploring social networks – Zachary's karate club dataset
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Exploring social networks – Twitter's mentions and retweets dataset
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Exploring biological networks – the C. Elegans neural network dataset
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Exploring biological networks – the yeast dataset
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Exploring the infrastructure domain – the airlines dataset
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Importing data from MySQL databases
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Importing data from Neo4j databases
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Importing data via NodeXL
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10. Exploring Some Useful Gephi Plugins
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10. Exploring Some Useful Gephi Plugins
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Introduction
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Exporting networks on the Web using Seadragon
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Exporting rich interactive visualizations using Sigma.js
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Describing complex network structures using GEXF
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Generating world maps
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Performing social network analysis
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Index
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Index

Installing Gephi

This recipe discusses the minimum system configurations required in order to install Gephi and the installation process for different platforms.

Getting ready

Gephi, being a network analysis and visualization tool, requires a compatible graphics card to be installed on your system. It uses a built-in OpenGL engine for fast processing when dealing with very large networks. Hence, it requires OpenGL 1.2 installed on your system. Gephi also requires Java 6 or later. Make sure you have these two programs installed on your system before you go ahead with the installation process.

How to do it…

Follow these steps to install Gephi on Windows:

  1. Download the Gephi installer from the official website: https://gephi.github.io.
  2. Run the installer and hit Next:
    How to do it…
  3. Accept the license agreement and hit Next:
    How to do it…
  4. Keep clicking on the Next button until you reach the following screen. Click on Install:
    How to do it…
  5. The installation will begin and once it's over, the following screen is displayed. Hit Finish to complete the setup:
    How to do it…

To install Gephi on a Linux machine, follow these steps:

  1. From Gephi's official website (https://gephi.github.io), download the TAR installer file.
  2. Once the download has finished, untar the file and run Gephi by executing ./bin/gephi.
  3. Ubuntu users can make use of the daily build, available from Launchpad. First, run sudo apt-add-repository ppa:rockclimb/gephi-daily to your software sources.
  4. Then, run sudo apt-get update, followed by sudo apt-get install gephi, in order to install Gephi on your box.

The installation process for Mac OS X is pretty simple and straightforward:

  1. From Gephi's official website (https://gephi.github.io), download the installer.
  2. Once the download has finished, double-click on the DMG file to run the installer.
  3. Once the installation has finished, a new window will open. Double-click on the Gephi icon to run the application.

There's more…

As mentioned earlier, Gephi is a cross-platform tool and works on many more platforms than the ones described in this recipe. If the graphs on which you are going to work are very large, then a 64-bit version of Gephi will have to be installed if you are also using a 64-bit machine.

One might face some issues while installing Gephi, most of which are related to memory management in Java. To learn about fixing some of the most common ones, refer to the next recipe, Troubleshooting the Gephi installation.

See also

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