Péter Érdi

Center for Complex Systems Studies, Kalamazoo College

1200 Academy st, Kalamazoo, 49006, MI, USA

Gábor Csárdi

Department of Biophysics, Research Institute for Nuclear and Particle Physics

29-33 Konkoly-Thege st, Budapest, H-1121, Hungary

Center for Complex Systems Studies, Kalamazoo College

1200 Academy st, Kalamazoo, 49006, MI, USA

Copyright (C) 2006 Péter Érdi and Gábor Csárdi Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with no Invariant Sections, no Front-Cover Texts, and no Back-Cover Texts. A copy of the license is included in the section entitled “GNU Free Documentation License”.


Table of Contents

Introduction
Graph Concepts and the igraph interface
Graph: vertices, edges
The igraph interface
GNU R, igraph and tkigraph
Starting tkigraph
Creating graphs
Loading and saving graphs
Adding a graph “by hand
Editing a graph
Plotting graphs
Protein-protein interaction networks
Regular Network Structures
Rings
Lattices
Trees
Stars
Full graph
Graph Atlas
Random Networks
Erdõs-Rényi random graphs
Scale-free graphs
The configuration model
The Watts-Strogatz small-world model
Network Centrality
Degree
Closeness
Betweenness
Edge betweenness
Network Components
Small World Networks
Scale-free Networks
Network Motifs
Assignments
The GNU Free Documentation License
0. PREAMBLE
1. APPLICABILITY AND DEFINITIONS
2. VERBATIM COPYING
3. COPYING IN QUANTITY
4. MODIFICATIONS
5. COMBINING DOCUMENTS
6. COLLECTIONS OF DOCUMENTS
7. AGGREGATION WITH INDEPENDENT WORKS
8. TRANSLATION
9. TERMINATION
10. FUTURE REVISIONS OF THIS LICENSE
G.1.1 ADDENDUM: How to use this License for your documents