Gephi
Resources for Gephi: Overview and explanations of Gephi Gephi’s overview tutorial An introductory video to create data for Gephi and to use degree, closeness and betweeness (also posted on the website unde today’s lecture). Gephi’s overview of layouts Basic navigation
Layouts Choose the appropriate layout so that visualization is meaningful. Common force directed (repulsion) ones: Force Atalas 2 (It is focused on being useful to explore and get meaning for real data, and a good readability, slow) Yifan Hu (similar to FA2, fast, good for large graphs) Fruchterman-Reingold (The nodes are the mass particles and the edges are springs between the particles. The algorithms try to minimize the energy of this physical system. It has become a standard but remains very slow.) OpenOrd layout (good for communities) Not force directed: Expansion Geographic map with GeoLayout
SAVE Once you have a visualization that you like, save the network, so that the next time you open it looks the same Cannot use undo in Gephi When you run an analysis, save the network again with a different name for future references When you open part of a network on a new tab in Gephi, save that as well.
Preview Tab Click Preview next to the Data Laboratory, you might like that view of the network better: If you export, then this is what you export:
Other metrics Average path length: under the statics module, right Computes the average of shortest paths between all pairs of nodes Result:
Filtering nodes based on degree Find Filters on the top right, next to Statistics Under topology, you can find the degree Choose one, drag and drop it to the Queries Choose the bounds needed.
Centralities Click diameter under Statistics module on the right Centralities that are available: Closeness PageRank HITS Betweeness For directed graphs, check:
Ranking nodes based on centralities Once you ran a metric, you can size/color the nodes based on your choices you ran. Under on the top left, choose Nodes and either size or color Depending on the version you run, you will see:
Export You can export the visualized graph as SVG or PDF: Go to preview (fix if needed) Resize for large networks Click SVG (SVG is vectorial graphics like PDF so they scale to different sizes nicely)