Gephi Cookbook电子书

Gephi Cookbook

Table of Contents

Gephi Cookbook

Credits

About the Author

Acknowledgments

About the Reviewers

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Preface

What this book covers

What you need for this book

Who this book is for

Sections

Getting ready

How to do it…

How it works…

There's more…

See also

Conventions

Reader feedback

Customer support

Downloading the color images of this book

Errata

Piracy

Questions

1. Getting Started with Gephi

Introduction

Installing Gephi

Getting ready

How to do it…

There's more…

See also

Troubleshooting the Gephi installation

How to do it…

How it works…

See also

Exploring Gephi's graphical user interface

Getting ready

How to do it…

How it works…

The basics of working in the Overview mode

Getting ready

How to do it…

See also

The basics of working in the Data Laboratory mode

Getting ready

How to do it…

See also

The basics of working in the Preview mode

Getting ready

How to do it…

See also

2. Basic Graph Manipulations

Introduction

Generating a random graph

How to do it…

There's more…

Selecting and highlighting nodes in the graph

How to do it…

How it works…

There's more…

Coloring and sizing nodes in the graph

How to do it…

How it works…

There's more…

Adding nodes and edges to the graph

How to do it…

How it works…

There's more…

Editing node attributes in the graph

How to do it…

There's more…

Finding out the shortest path in the graph

Getting ready

How to do it…

How it works…

There's more…

See also

Setting the edge and label properties

How to do it…

Setting basic properties for graphs, nodes, edges, and labels

Getting ready

How to do it…

Changing the background color of the graph

How to do it…

Generating a heat map for the graph

Getting ready

How to do it…

How it works…

There's more…

Showing convex hulls for a graph where a hierarchy exists

How to do it…

There's more…

See also

Showing/hiding various parts of the graph

How to do it…

How it works…

Reverting changes in the graph to the original presets

Getting ready

How to do it…

See also

Creating a PNG file directly from the graph window in user-specified sizes

Getting ready

How to do it…

How it works…

There's more…

See also

3. Using Graph Layout Algorithms

Introduction

Using the Clockwise Rotate layout algorithm

Getting ready

How to do it…

How it works…

There's more…

See also

Using the Counter-Clockwise Rotate layout algorithm

How to do it…

How it works…

There's more…

See also

Using the Contraction layout algorithm

How to do it…

How it works…

There's more…

See also

Using the Expansion layout algorithm

How to do it…

How it works…

There's more…

See also

Using the Force Atlas layout algorithm

How to do it…

How it works…

There's more…

There's more…

See also

Using the Force Atlas 2 layout algorithm

How to do it…

How it works…

There's more…

See also

Using the Fruchterman Reingold layout algorithm

How to do it…

How it works…

There's more…

See also

Using the Label Adjust layout algorithm

How to do it…

How it works…

There's more…

See also

Using the Random Layout algorithm

How to do it…

Using the Yifan Hu layout algorithm

How to do it…

How it works…

There's more…

See also

Using the Yifan Hu Proportional layout algorithm

How to do it…

See also

Using the Yifan Hu Multilevel layout algorithm

How to do it…

How it works…

There's more…

See also

4. Working with Partition and Ranking Algorithms

Introduction

Partitioning the graph based on node attributes

Getting ready

How to do it…

How it works…

There's more…

See also

Partitioning the graph based on edge attributes

Getting ready

How to do it…

How it works…

There's more…

Configuring node colors in a graph by ranking nodes

Getting ready

How to do it…

How it works…

See also

Configuring node sizes in a graph by ranking nodes

How to do it…

How it works…

Configuring node label colors in a graph by ranking nodes

Getting ready

How to do it…

How it works…

Configuring node label sizes in a graph by ranking nodes

Getting ready

How to do it…

How it works…

Configuring edge colors in a graph by ranking edges

How to do it…

How it works…

Configuring the colors of edge labels in a graph by ranking edges

Getting ready

How to do it…

How it works…

Configuring the size of edge labels in a graph by ranking edges

Getting ready

How to do it…

5. Running Metrics, Filters, and Timelines

Introduction

Selecting a list of metrics for a graph

Getting ready

How to do it…

Finding the average degree and average weighted degree of a graph

How to do it…

How it works…

There's more…

See also

Finding the network diameter

How to do it…

How it works…

There's more…

See also

Finding graph density

How to do it…

How it works…

There's more…

Finding the HITS value for a graph

How to do it…

How it works…

There's more…

See also

Finding a graph's modularity

How to do it…

How it works…

See also

Finding a graph's PageRank

How to do it…

How it works…

See also

Finding connected components in a graph

How to do it…

How it works…

There's more…

See also

Getting a node overview of a graph

How to do it…

How it works…

See also

Getting an edge overview of a graph

How to do it…

Getting dynamic statistics for a graph

Getting ready

How to do it…

Applying individual filters on a graph

How to do it…

How it works…

Applying a combination of filters on a graph

How to do it…

How it works…

There's more…

Filtering dynamic graphs based on time intervals

Getting ready

How to do it…

See also

6. Working in the Data Laboratory Mode

Introduction

Importing a spreadsheet

Getting ready

How to do it…

How it works…

Adding and deleting nodes in a graph

Getting ready

How to do it…

Changing the attributes of an existing node in a graph

Getting ready

How to do it…

Adding and deleting edges in a graph

Getting ready

How to do it…

How it works…

There's more…

Changing the attributes of an existing edge in a graph

How to do it…

Adding/deleting columns

Getting ready

How to do it…

There's more…

Merging columns

Getting ready

How to do it…

How it works…

Copying data between columns

Getting ready

How to do it…

There's more…

Filtering, searching, and modifying data based on particular attributes

Getting ready

How to do it…

How it works…

See also

Creating columns with dynamic regular expression filtering

Getting ready

How to do it…

How it works…

Exporting a table

Getting ready

How to do it…

7. Getting Graphs and Networks Ready for Preview

Introduction

Previewing and fine-tuning a graph in the Default mode

Getting ready

How to do it…

How it works…

There's more…

Previewing and fine-tuning a graph in the Default Curved mode

Getting ready

How to do it…

How it works…

There's more…

Previewing and fine-tuning a graph in the Default Straight mode

Getting ready

How to do it…

How it works…

Previewing and fine-tuning a graph in the Text outline mode

Getting ready

How to do it…

How it works…

Previewing and fine-tuning a graph in the Black Background mode

Getting ready

How to do it…

How it works…

Previewing and fine-tuning a graph in the Edges Custom Color mode

Getting ready

How to do it…

How it works…

There's more…

Previewing and fine-tuning a graph in the Tag Cloud mode

Getting ready

How to do it…

How it works…

Exporting a graph in the SVG, PNG, or PDF format

Getting ready

How to do it…

How it works…

There's more…

8. Exploring Dynamic and Multilevel Graphs

Introduction

Building dynamic/temporal graphs in Gephi

How to do it…

How it works…

There's more…

See also

Working with dynamic/temporal graphs

Getting ready

How to do it…

How it works…

There's more…

See also

Working with multilevel graphs

How to do it…

How it works…

See also

Expanding and contracting subgraphs in metanodes

Getting ready

How to do it…

How it works…

Clustering links and attributes

How to do it…

9. Getting Real-world Graph Datasets

Introduction

Exploring the Web and Internet domain – EuroSiS Web mapping study

Getting ready

How to do it…

How it works…

See also

Exploring the Web and Internet domain – the Internet dataset

Getting ready

How to do it…

How it works…

There's more…

See also

Exploring social networks – Zachary's karate club dataset

Getting ready

How to do it…

How it works…

There's more…

See also

Exploring social networks – Twitter's mentions and retweets dataset

Getting ready

How to do it…

How it works…

There's more…

Exploring biological networks – the C. Elegans neural network dataset

Getting ready

How to do it…

How it works…

See also

Exploring biological networks – the yeast dataset

Getting ready

How to do it…

How it works…

See also

Exploring the infrastructure domain – the airlines dataset

Getting ready

How to do it…

How it works…

Importing data from MySQL databases

Getting ready

How to do it…

How it works…

See also

Importing data from Neo4j databases

Getting ready

How to do it…

How it works…

See also

Importing data via NodeXL

Getting ready

How to do it…

How it works…

See also

10. Exploring Some Useful Gephi Plugins

Introduction

Exporting networks on the Web using Seadragon

Getting ready

How to do it…

How it works…

There's more…

See also

Exporting rich interactive visualizations using Sigma.js

Getting ready

How to do it…

How it works…

See also

Describing complex network structures using GEXF

How to do it…

How it works…

See also

Generating world maps

Getting ready

How to do it…

How it works…

See also

Performing social network analysis

Getting ready

How to do it…

How it works…

There's more…

See also

Index