Browse Library
Sign In Start Free Trial
Close icon Search icon
Account
Browse Library Sign In Start Free Trial

Add to playlist

Create a Playlist

Modal Close icon
You need to login to use this feature.
  • Book Overview & Buying Gephi Cookbook
  • Table Of Contents Toc
Gephi Cookbook

Gephi Cookbook

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

Troubleshooting the Gephi installation

While installing Gephi, there are a couple of problems that users encounter quite frequently, most of which are related to memory-specific requirements. Some of these issues are discussed in this recipe, along with the fixes that one can employ to resolve them.

How to do it…

If you encounter any memory- or JVM-related issues, try following these steps to check if the issue can be resolved:

  1. If you are using Java 8, try downgrading to Java 7 and check whether the problem is resolved.
  2. If you are using the latest version of Gephi, uninstall it and install an older version. If these two fixes do not resolve the problem, then you might need to do operating system-specific fixes, as listed in the following points:
    • For Windows systems, go to the Gephi folder in Program Files in C:\ and then go to the etc folder. Open the gephi.conf file in Notepad. In the default options, change the -J-Xmx512m value to -J-Xmx1024m. This changes the maximum heap size allocated to Java to 1,024 MB. If you are using a 64-bit machine, the gephi.conf file will be located in the Gephi folder in C:\Program Files(x86).
    • For Linux systems, go to the etc folder in the Gephi application directory and open the gephi.conf file. Change the -J-Xmx512m value to -J-Xmx1024m to change the maximum heap size allocated to Java to 1,024 MB.
    • For Mac OS X systems, go to Show Package Contents by right-clicking on the Gephi icon in the Applications folder. Inside the Contents folder, go to the Resources/Gephi/etc folder. Open the gephi.conf file and, in the default options, change the -J-Xmx512m value to -J-Xmx1024m. This changes the maximum heap size allocated to Java to 1,024 MB.

Tip

Unable to save the modified gephi.conf file? Open your text editor in administrator mode, navigate to the folder where the file is located, open the file, and then make the changes. Finally, hit Save to save the changes.

How it works…

Java Virtual Machine (JVM) is an abstract computing machine, otherwise known as a virtual machine. A virtual machine emulates a part of the computing system. JVM executes a Java program compiled into Java bytecode. Since Gephi runs on JVM, its functioning depends on the memory allocated in the system for Java. If very little memory has been allocated to Java, it won't have enough resources to load all the data and, hence, the application won't start. On the other hand, if too much memory has been allocated to Java, then the system won't let Java start and will throw the "JVM Creation failed" message.

See also

CONTINUE READING
83
Tech Concepts
36
Programming languages
73
Tech Tools
Icon Unlimited access to the largest independent learning library in tech of over 8,000 expert-authored tech books and videos.
Icon Innovative learning tools, including AI book assistants, code context explainers, and text-to-speech.
Icon 50+ new titles added per month and exclusive early access to books as they are being written.
Gephi Cookbook
End of Section 1
Next Section
notes
bookmark Notes and Bookmarks search Search in title playlist Add to playlist font-size Font size

Change the font size

margin-width Margin width

Change margin width

day-mode Day/Sepia/Night Modes

Change background colour

Close icon Search
Country selected
Close icon Your notes and bookmarks

Confirmation

Modal Close icon
claim successful
Order Page Read Now

Buy this book with your credits?

Modal Close icon
Are you sure you want to buy this book with one of your credits?
Close
YES, BUY

Submit Your Feedback

Modal Close icon
Modal Close icon
Modal Close icon