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Gephi Cookbook

Book Description

Over 90 hands-on recipes to master the art of network analysis and visualization with Gephi

In Detail

Gephi is an open source, user-friendly network visualization and analysis tool that provides numerous powerful features, making it easy for novices to get to grips with graph analysis quickly.

This book is your one-stop guide to learning Gephi's interactive networking and visualization, alongside the graph theory concepts that drive them. Each recipe walks you through a task and explains why and how it works. Starting with installing Gephi, you will learn how to begin analyzing a graph using Gephi's various features. You will discover how to make informed decisions using layout algorithms and filters, and perform statistical analysis with real-world datasets. This guide is an invaluable resource if you would like to plunge into the network analysis domain without having to learn how to code.

What You Will Learn

  • Install and configure Gephi on your system and understand its various features

  • Perform basic manipulation and exploration tasks on graphs

  • Understand various layout algorithms present by default in Gephi and the principles behind them

  • Explore the properties of graphical networks using numerous filters and statistical metrics available in Gephi

  • Import graph data from different sources and manipulate it directly in tabular formats

  • Use real-world datasets to better understand network analysis

  • Downloading the example code for this book. You can download the example code files for all Packt books you have purchased from your account at http://www.PacktPub.com. If you purchased this book elsewhere, you can visit http://www.PacktPub.com/support and register to have the files e-mailed directly to you.

    Table of Contents

    1. Gephi Cookbook
      1. Table of Contents
      2. Gephi Cookbook
      3. Credits
      4. About the Author
      5. Acknowledgments
      6. About the Reviewers
      7. www.PacktPub.com
        1. Support files, eBooks, discount offers, and more
          1. Why Subscribe?
          2. Free Access for Packt account holders
      8. Preface
        1. What this book covers
        2. What you need for this book
        3. Who this book is for
        4. Sections
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
          5. See also
        5. Conventions
        6. Reader feedback
        7. Customer support
          1. Downloading the color images of this book
          2. Errata
          3. Piracy
          4. Questions
      9. 1. Getting Started with Gephi
        1. Introduction
        2. Installing Gephi
          1. Getting ready
          2. How to do it…
          3. There's more…
          4. See also
        3. Troubleshooting the Gephi installation
          1. How to do it…
          2. How it works…
          3. See also
        4. Exploring Gephi's graphical user interface
          1. Getting ready
          2. How to do it…
          3. How it works…
        5. The basics of working in the Overview mode
          1. Getting ready
          2. How to do it…
          3. See also
        6. The basics of working in the Data Laboratory mode
          1. Getting ready
          2. How to do it…
          3. See also
        7. The basics of working in the Preview mode
          1. Getting ready
          2. How to do it…
          3. See also
      10. 2. Basic Graph Manipulations
        1. Introduction
        2. Generating a random graph
          1. How to do it…
          2. There's more…
        3. Selecting and highlighting nodes in the graph
          1. How to do it…
          2. How it works…
          3. There's more…
        4. Coloring and sizing nodes in the graph
          1. How to do it…
          2. How it works…
          3. There's more…
        5. Adding nodes and edges to the graph
          1. How to do it…
          2. How it works…
          3. There's more…
        6. Editing node attributes in the graph
          1. How to do it…
          2. There's more…
        7. Finding out the shortest path in the graph
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
          5. See also
        8. Setting the edge and label properties
          1. How to do it…
        9. Setting basic properties for graphs, nodes, edges, and labels
          1. Getting ready
          2. How to do it…
        10. Changing the background color of the graph
          1. How to do it…
        11. Generating a heat map for the graph
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
        12. Showing convex hulls for a graph where a hierarchy exists
          1. How to do it…
          2. There's more…
          3. See also
        13. Showing/hiding various parts of the graph
          1. How to do it…
          2. How it works…
        14. Reverting changes in the graph to the original presets
          1. Getting ready
          2. How to do it…
          3. See also
        15. Creating a PNG file directly from the graph window in user-specified sizes
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
          5. See also
      11. 3. Using Graph Layout Algorithms
        1. Introduction
        2. Using the Clockwise Rotate layout algorithm
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
          5. See also
        3. Using the Counter-Clockwise Rotate layout algorithm
          1. How to do it…
          2. How it works…
          3. There's more…
          4. See also
        4. Using the Contraction layout algorithm
          1. How to do it…
          2. How it works…
          3. There's more…
          4. See also
        5. Using the Expansion layout algorithm
          1. How to do it…
          2. How it works…
          3. There's more…
          4. See also
        6. Using the Force Atlas layout algorithm
          1. How to do it…
          2. How it works…
          3. There's more…
          4. There's more…
          5. See also
        7. Using the Force Atlas 2 layout algorithm
          1. How to do it…
          2. How it works…
          3. There's more…
          4. See also
        8. Using the Fruchterman Reingold layout algorithm
          1. How to do it…
          2. How it works…
          3. There's more…
          4. See also
        9. Using the Label Adjust layout algorithm
          1. How to do it…
          2. How it works…
          3. There's more…
          4. See also
        10. Using the Random Layout algorithm
          1. How to do it…
        11. Using the Yifan Hu layout algorithm
          1. How to do it…
          2. How it works…
          3. There's more…
          4. See also
        12. Using the Yifan Hu Proportional layout algorithm
          1. How to do it…
          2. See also
        13. Using the Yifan Hu Multilevel layout algorithm
          1. How to do it…
          2. How it works…
          3. There's more…
          4. See also
      12. 4. Working with Partition and Ranking Algorithms
        1. Introduction
        2. Partitioning the graph based on node attributes
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
          5. See also
        3. Partitioning the graph based on edge attributes
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
        4. Configuring node colors in a graph by ranking nodes
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. See also
        5. Configuring node sizes in a graph by ranking nodes
          1. How to do it…
          2. How it works…
        6. Configuring node label colors in a graph by ranking nodes
          1. Getting ready
          2. How to do it…
          3. How it works…
        7. Configuring node label sizes in a graph by ranking nodes
          1. Getting ready
          2. How to do it…
          3. How it works…
        8. Configuring edge colors in a graph by ranking edges
          1. How to do it…
          2. How it works…
        9. Configuring the colors of edge labels in a graph by ranking edges
          1. Getting ready
          2. How to do it…
          3. How it works…
        10. Configuring the size of edge labels in a graph by ranking edges
          1. Getting ready
          2. How to do it…
      13. 5. Running Metrics, Filters, and Timelines
        1. Introduction
        2. Selecting a list of metrics for a graph
          1. Getting ready
          2. How to do it…
        3. Finding the average degree and average weighted degree of a graph
          1. How to do it…
          2. How it works…
          3. There's more…
          4. See also
        4. Finding the network diameter
          1. How to do it…
          2. How it works…
          3. There's more…
          4. See also
        5. Finding graph density
          1. How to do it…
          2. How it works…
          3. There's more…
        6. Finding the HITS value for a graph
          1. How to do it…
          2. How it works…
          3. There's more…
          4. See also
        7. Finding a graph's modularity
          1. How to do it…
          2. How it works…
          3. See also
        8. Finding a graph's PageRank
          1. How to do it…
          2. How it works…
          3. See also
        9. Finding connected components in a graph
          1. How to do it…
          2. How it works…
          3. There's more…
          4. See also
        10. Getting a node overview of a graph
          1. How to do it…
          2. How it works…
          3. See also
        11. Getting an edge overview of a graph
          1. How to do it…
        12. Getting dynamic statistics for a graph
          1. Getting ready
          2. How to do it…
        13. Applying individual filters on a graph
          1. How to do it…
          2. How it works…
        14. Applying a combination of filters on a graph
          1. How to do it…
          2. How it works…
          3. There's more…
        15. Filtering dynamic graphs based on time intervals
          1. Getting ready
          2. How to do it…
          3. See also
      14. 6. Working in the Data Laboratory Mode
        1. Introduction
        2. Importing a spreadsheet
          1. Getting ready
          2. How to do it…
          3. How it works…
        3. Adding and deleting nodes in a graph
          1. Getting ready
          2. How to do it…
        4. Changing the attributes of an existing node in a graph
          1. Getting ready
          2. How to do it…
        5. Adding and deleting edges in a graph
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
        6. Changing the attributes of an existing edge in a graph
          1. How to do it…
        7. Adding/deleting columns
          1. Getting ready
          2. How to do it…
          3. There's more…
        8. Merging columns
          1. Getting ready
          2. How to do it…
          3. How it works…
        9. Copying data between columns
          1. Getting ready
          2. How to do it…
          3. There's more…
        10. Filtering, searching, and modifying data based on particular attributes
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. See also
        11. Creating columns with dynamic regular expression filtering
          1. Getting ready
          2. How to do it…
          3. How it works…
        12. Exporting a table
          1. Getting ready
          2. How to do it…
      15. 7. Getting Graphs and Networks Ready for Preview
        1. Introduction
        2. Previewing and fine-tuning a graph in the Default mode
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
        3. Previewing and fine-tuning a graph in the Default Curved mode
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
        4. Previewing and fine-tuning a graph in the Default Straight mode
          1. Getting ready
          2. How to do it…
          3. How it works…
        5. Previewing and fine-tuning a graph in the Text outline mode
          1. Getting ready
          2. How to do it…
          3. How it works…
        6. Previewing and fine-tuning a graph in the Black Background mode
          1. Getting ready
          2. How to do it…
          3. How it works…
        7. Previewing and fine-tuning a graph in the Edges Custom Color mode
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
        8. Previewing and fine-tuning a graph in the Tag Cloud mode
          1. Getting ready
          2. How to do it…
          3. How it works…
        9. Exporting a graph in the SVG, PNG, or PDF format
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
      16. 8. Exploring Dynamic and Multilevel Graphs
        1. Introduction
        2. Building dynamic/temporal graphs in Gephi
          1. How to do it…
          2. How it works…
          3. There's more…
          4. See also
        3. Working with dynamic/temporal graphs
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
          5. See also
        4. Working with multilevel graphs
          1. How to do it…
          2. How it works…
          3. See also
        5. Expanding and contracting subgraphs in metanodes
          1. Getting ready
          2. How to do it…
          3. How it works…
        6. Clustering links and attributes
          1. How to do it…
      17. 9. Getting Real-world Graph Datasets
        1. Introduction
        2. Exploring the Web and Internet domain – EuroSiS Web mapping study
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. See also
        3. Exploring the Web and Internet domain – the Internet dataset
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
          5. See also
        4. Exploring social networks – Zachary's karate club dataset
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
          5. See also
        5. Exploring social networks – Twitter's mentions and retweets dataset
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
        6. Exploring biological networks – the C. Elegans neural network dataset
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. See also
        7. Exploring biological networks – the yeast dataset
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. See also
        8. Exploring the infrastructure domain – the airlines dataset
          1. Getting ready
          2. How to do it…
          3. How it works…
        9. Importing data from MySQL databases
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. See also
        10. Importing data from Neo4j databases
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. See also
        11. Importing data via NodeXL
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. See also
      18. 10. Exploring Some Useful Gephi Plugins
        1. Introduction
        2. Exporting networks on the Web using Seadragon
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
          5. See also
        3. Exporting rich interactive visualizations using Sigma.js
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. See also
        4. Describing complex network structures using GEXF
          1. How to do it…
          2. How it works…
          3. See also
        5. Generating world maps
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. See also
        6. Performing social network analysis
          1. Getting ready
          2. How to do it…
          3. How it works…
          4. There's more…
          5. See also
      19. Index