Gephi Tutorial Layouts * Introduction Layouts * Install plugins - PowerPoint PPT Presentation

Tutorial Gephi Tutorial Layouts * Introduction Layouts * Install plugins * Import fjle * Run * Choice * ForceAtlas Welcome to this advanced tutorial. It will teach you the fjne 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 fjle • Go to the Tools menu and then Plugins. * Run * Choice • In the Available Plugins tab check: * ForceAtlas - 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 and you are asked to reboot Gephi. Click * Geographic map OK. * Node overlapping * Geometric transform * Save * Conclusion

Tutorial Layouts Open Graph File * Introduction • Download the fjle LesMiserables.gexf * Install plugins • In the menubar, go to File Menu and Open... * Import fjle * Run • When your fjle is opened, the report sums up data found and any issues. * Choice * ForceAtlas - Number of nodes - Number of edges * Fruchterman-Reingold - Type of graph * YifanHu Multilevel * 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” dataset 1 . This is a coappearance weighted network of characters in the novel “Les Miserables” from Victor Hugo. * Install plugins * Import fjle * Run * Choice * ForceAtlas * Fruchterman-Reingold * YifanHu Multilevel * OpenOrd * ForceAtlas 2 * Circular Layout * Radial Axis Layout * Geographic map * Node overlapping Node position is random at fjrst, so you may see a slighty different representation. * Geometric transform * Save * Conclusion 1 D. E. Knuth, The Stanford GraphBase: A Platform for Combinatorial Computing, Addison-Wesley, Reading, MA (1993).

Tutorial Layouts Run a layout Layout algorithms set the graph shape, it is the most essential operation. * Introduction * Install plugins • Locate the Layout module, on the left panel. * Import fjle * Run • Choose “Force Atlas” * Choice * ForceAtlas You can see the layout properties below, leave default * Fruchterman-Reingold values. * YifanHu Multilevel * 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 The purpose of Layout Properties is to let you control the algorithm in order to make a * Introduction readable representation. * Install plugins * Import fjle * Run • Set the “Repulsion strengh” at 10 000 to expand * Choice the graph. * ForceAtlas • Type “Enter” to validate the changed value. * Fruchterman-Reingold * YifanHu Multilevel * OpenOrd * ForceAtlas 2 * Circular Layout * Radial Axis Layout • And now the algorithm. * Geographic map * 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 fjle * 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! Run the layout again and drag the nodes to stress it. * Introduction * Install plugins • Locate Dragging action, in the top left of the * Import fjle Visualization panel. * Run * Choice • Ajust the selection diameter in the panel or by * ForceAtlas 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 • And now the algorithm. * Radial Axis Layout * 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. OpenOrd ForceAtlas 2 * Install plugins * Import fjle * Run * Choice * ForceAtlas * Fruchterman-Reingold * YifanHu Multilevel * OpenOrd * ForceAtlas 2 * Circular Layout * Radial Axis Layout Radial Axis GeoLayout * Geographic map * Node overlapping * Geometric transform * Save * Conclusion Airlines sample dataset: http://gephi.org/datasets/airlines-sample.gexf

Tutorial Layouts So how to choose a layout? In general, select one according to the feature of the topology you want to highlight: * Introduction * Install plugins * Import fjle emphasis * Run emphasis * Choice DIVISIONS COMPLEMENTARITIES * ForceAtlas * Fruchterman-Reingold ForceAtlas, Yifan Hu, * YifanHu Multilevel OpenOrd Frushterman-Reingold * OpenOrd * ForceAtlas 2 emphasis * Circular Layout emphasis * Radial Axis Layout GEOGRAPHIC * Geographic map RANKING * Node overlapping REPARTITION * Geometric transform * Save Circular, Radial Axis GeoLayout * Conclusion Graphic Adjustements - Label Adjust - Expansion - Noverlap - Contraction

Tutorial Layouts ForceAtlas layout Home-brew layout of Gephi, it is made to spatialize Small-World / Scale-free networks. * Introduction It is focused on quality (meaning “being useful to explore real data”) to allow a rigor - * Install plugins ous interpretation of the graph (e.g. in SNA) with the fewest biases possible, and a good * Import fjle readability even if it is slow. * Run * Choice Author: Mathieu Jacomy * ForceAtlas Date: 2007 * Fruchterman-Reingold Kind: Force-directed Complexity: O(N²) * YifanHu Multilevel Graph size: 1 to 10 000 nodes * OpenOrd Use edge weight: Yes * ForceAtlas 2 * 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 fjle • 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- sion of disconnected components. * Circular Layout * Radial Axis Layout • Attraction Distrib. = checked Push hubs (high number of output links) at the * Geographic map periphery and put authorities (high number of in - * Node overlapping 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 the edges are springs between the particles. The algorithms try to minimize the energy * Install plugins of this physical system. It has become a standard but remains very slow. * Import fjle * Run * Choice Author: Thomas Fruchterman & Edward Reingold 1 * ForceAtlas Date: 1991 * Fruchterman-Reingold Kind: Force-directed * YifanHu Multilevel Complexity: O(N²) Graph size: 1 to 1 000 nodes * OpenOrd Use edge weight: No * ForceAtlas 2 * 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).