Tutorial Layouts Gephi Tutorial * Introduction * Install plugins * Import file Layouts * Run * Choice * ForceAtlas Welcome to this advanced tutorial. It will teach you the fine art of network * Fruchterman-Reingold layout in Gephi: how to use algorithms that place the nodes inside the graphic space. * YifanHu Multilevel * OpenOrd Gephi version 0.8alpha was used to do this tutorial. * ForceAtlas 2 * Circular Layout Get Gephi * Radial Axis Layout * Geographic map * Node overlapping * Geometric transform * Save * Conclusion Last updated June 13th, 2011 Tutorial Layouts Install layout plugins * Introduction We need to install additional plugins. * Install plugins * Import file * Run • Go to the Tools menu and then Plugins. * Choice * ForceAtlas • In the Available Plugins tab check: - OpenOrdLayout * Fruchterman-Reingold - CircularLayout * YifanHu Multilevel - GeoLayout * OpenOrd - Geometric Transformation * ForceAtlas 2 - NoverlapLayout * Circular Layout * Radial Axis Layout • Click on Install. The plugins are installed * Geographic map and you are asked to reboot Gephi. Click * Node overlapping OK. * Geometric transform * Save * Conclusion Tutorial Layouts Open Graph File * Introduction • Download the file LesMiserables.gexf * Install plugins * Import file • In the menubar, go to File Menu and Open... * Run * Choice • When your file is opened, the report sums up data found and any issues. * ForceAtlas - Number of nodes * Fruchterman-Reingold - Number of edges * YifanHu Multilevel - Type of graph * OpenOrd • Click on OK to validate and see the graph. * ForceAtlas 2 * Circular Layout * Radial Axis Layout * Geographic map * Node overlapping * Geometric transform * Save Graph Format * Conclusion - GEXF - Tulip TLP - GraphML - CSV - Pajek NET - Netdraw VNA - GDF - Compressed ZIP/GZ - GML Tutorial Layouts You should now see a graph * Introduction We imported the “Les Miserables” dataset1. This is a coappearance weighted network of * Install plugins characters in the novel “Les Miserables” from Victor Hugo. * Import file * Run * Choice * ForceAtlas * Fruchterman-Reingold * YifanHu Multilevel * OpenOrd * ForceAtlas 2 * Circular Layout * Radial Axis Layout * Geographic map * Node overlapping * Geometric transform Node position is random at first, so you may see a slighty different representation. * Save * Conclusion 1 D. E. Knuth, The Stanford GraphBase: A Platform for Combinatorial Computing, Addison-Wesley, Reading, MA (1993). Tutorial Layouts Run a layout * Introduction Layout algorithms set the graph shape, it is the most essential operation. * Install plugins * Import file • Locate the Layout module, on the left panel. * Run * Choice • Choose “Force Atlas” * ForceAtlas * Fruchterman-Reingold You can see the layout properties below, leave default * YifanHu Multilevel values. * OpenOrd * ForceAtlas 2 • Click on to launch the algorithm. * Circular Layout * Radial Axis Layout * Geographic map • You see now the positions of nodes changing in real time. * Node overlapping * Geometric transform * Save * Conclusion Layout algorithms Graphs are usually laid out with “Force-based” algorithms. They follow a simple principle: linked nodes attract each other and non-linked nodes are pushed apart. Tutorial Layouts Control the layout * Introduction The purpose of Layout Properties is to let you control the algorithm in order to make a * Install plugins readable representation. * Import file * Run • Set the “Repulsion strengh” at 10 000 to expand * Choice the graph. * ForceAtlas * Fruchterman-Reingold • Type “Enter” to validate the changed value. * YifanHu Multilevel * OpenOrd * ForceAtlas 2 * Circular Layout * Radial Axis Layout * Geographic map • And now the algorithm. * Node overlapping * Geometric transform * Save * Conclusion Tips Click on the icon “Center on Graph” on the bottom left of the Visualization panel if you don’t see the graph anymore. Tutorial Layouts You should now see a graph with the layout applied * Introduction * Install plugins * Import file * Run * Choice * ForceAtlas * Fruchterman-Reingold * YifanHu Multilevel * OpenOrd * ForceAtlas 2 * Circular Layout * Radial Axis Layout * Geographic map * Node overlapping * Geometric transform * Save * Conclusion Tutorial Layouts Play against the algorithm! * Introduction Run the layout again and drag the nodes to stress it. * Install plugins * Import file • Locate Dragging action, in the top left of the * Run Visualization panel. * Choice * ForceAtlas • Ajust the selection diameter in the panel or by using the shortcut “Ctrl + Mouse Wheel”. * Fruchterman-Reingold * YifanHu Multilevel * OpenOrd Increase the “Autostab strength” in the Layout Properties to 100 000, then drag the * ForceAtlas 2 nodes. The graph becomes less deformed. * Circular Layout * Radial Axis Layout • And now the algorithm. * Geographic map * Node overlapping * Geometric transform * Save * Conclusion Tutorial Layouts Various layouts exist * Introduction Gephi implements various layout algorithms. They set the shape of the graph. * Install plugins * Import file OpenOrd ForceAtlas 2 * Run * Choice * ForceAtlas * Fruchterman-Reingold * YifanHu Multilevel * OpenOrd * ForceAtlas 2 * Circular Layout * Radial Axis Layout * Geographic map Radial Axis GeoLayout * Node overlapping * Geometric transform * Save * Conclusion Airlines sample dataset: http://gephi.org/datasets/airlines-sample.gexf Tutorial Layouts So how to choose a layout? * Introduction In general, select one according to the feature of the topology you want to highlight: * Install plugins * Import file * Run * Choice emphasis emphasis * ForceAtlas * Fruchterman-Reingold DIVISIONS COMPLEMENTARITIES ForceAtlas, Yifan Hu, * YifanHu Multilevel OpenOrd Frushterman-Reingold * OpenOrd * ForceAtlas 2 * Circular Layout * Radial Axis Layout emphasis * Geographic map emphasis * Node overlapping GEOGRAPHIC * Geometric transform RANKING REPARTITION * Save Circular, Radial Axis GeoLayout * Conclusion Graphic Adjustements - Label Adjust - Expansion - Noverlap - Contraction Tutorial Layouts ForceAtlas layout * Introduction Home-brew layout of Gephi, it is made to spatialize Small-World / Scale-free networks. * Install plugins It is focused on quality (meaning “being useful to explore real data”) to allow a rigor- * Import file ous interpretation of the graph (e.g. in SNA) with the fewest biases possible, and a good * Run readability even if it is slow. * Choice Author: Mathieu Jacomy * ForceAtlas Date: 2007 * Fruchterman-Reingold Kind: Force-directed * YifanHu Multilevel Complexity: O(N²) * OpenOrd Graph size: 1 to 10 000 nodes * ForceAtlas 2 Use edge weight: Yes * Circular Layout * Radial Axis Layout * Geographic map * Node overlapping * Geometric transform * Save * Conclusion Tutorial Layouts Run ForceAtlas * Introduction the layout by applying the following settings step by step: * Install plugins * Import file • Autostab strength = 2 000 Increase to move the nodes slowly. * Run * Choice • Repulsion strength = 1 000 How strongly does each node reject others. * ForceAtlas * Fruchterman-Reingold • Attraction strength = 1 How strongly each pair of connected nodes at- * YifanHu Multilevel tract each other. * OpenOrd * ForceAtlas 2 • Gravity = 100 Attract all nodes to the center to avoid disper- * Circular Layout sion of disconnected components. * Radial Axis Layout * Geographic map • Attraction Distrib. = checked Push hubs (high number of output links) at the * Node overlapping periphery and put authorities (high number of in- put links) more central. * Geometric transform * Save And now the algorithm. * Conclusion Adjust by Sizes This option avoids node overlapping, depending on the size of each node. Tutorial Layouts Fruchterman-Reingold layout * Introduction It simulates the graph as a system of mass particles. The nodes are the mass particles and * Install plugins the edges are springs between the particles. The algorithms try to minimize the energy * Import file of this physical system. It has become a standard but remains very slow. * Run * Choice Author: Thomas Fruchterman & Edward Reingold1 * ForceAtlas Date: 1991 * Fruchterman-Reingold Kind: Force-directed * YifanHu Multilevel Complexity: O(N²) * OpenOrd Graph size: 1 to 1 000 nodes * ForceAtlas 2 Use edge weight: No * Circular Layout * Radial Axis Layout * Geographic map * Node overlapping * Geometric transform * Save * Conclusion 1 Fruchterman, T. M. J., & Reingold, E. M. (1991). Graph Drawing by Force-Directed Placement. Software: Practice and Experience, 21(11). Tutorial Layouts Run Fruchterman-Reingold * Introduction the layout by applying the following settings step by step: * Install plugins * Import file * Run • Area = 100 Graph size area. * Choice • Area = 100 000 * ForceAtlas * Fruchterman-Reingold * YifanHu Multilevel • Gravity = 1 000 Attract all nodes to the center to avoid dispersion * OpenOrd • Gravity = 100 of disconnected components. * ForceAtlas 2 * Circular Layout * Radial Axis Layout * Geographic map * Node overlapping And now the algorithm. * Geometric transform * Save * Conclusion Unstable nodes position! Sometimes the algorithm does not converge, resulting in an unstable graph. Reduce the “Speed” setting to gain precision. Tutorial Layouts Yifan Hu Multilevel layout * Introduction It is a very fast algorithm with a good quality on large graphs. It combines a force-directed * Install plugins model with a graph coarsening technique (multilevel algorithm) to reduce the complex- * Import file ity. The repulsive forces on one node from a cluster of distant nodes are approximated by * Run a Barnes-Hut