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Multithreaded Gephi Force Atlas2 Layout in 2 or 3-d

Features

  • Parallel Barnes-Hut tree building
  • Computes total distance that all points move at each iteration in order to determine when the algorithm has converged
  • Parallel force, attraction, and speed computations
  • Option to rebuild Barnes-Hut tree every n iterations
  • Option to update Barnes-Hut tree centers every n iterations
  • Command line interface

Installation

Download gephi-toolkit-0.9.2-all.jar and forceatlas2.jar from https://github.com/klarman-cell-observatory/forceatlas2/releases

Command Line Usage

java -Djava.awt.headless=true -Xmx8g -cp forceatlas2.jar:gephi-toolkit-0.9.2-all.jar kco.forceatlas2.Main flags

where flags are

Flag Description Default Value
--input Input graph in one of Gephi input file formats https://gephi.org/users/supported-graph-formats/
--output Output file
--nsteps Number of iterations. Mutually exclusive with --targetChangePerNode
--targetChangePerNode Target distance change per node before stop the algorithm. Mutually exclusive with --nsteps
--targetSteps Maximum number of iterations before stopping the algoritm. This option is together with --targetChangePerNode 10000
--2d Whether to produce a 2d layout false
--directed Whether input graph is directed false
--nthreads Number of threads to use. All cores
--format Output file format. One of csv, gdf, gexf, gml, graphml, pajek, txt txt
--coords Tab separated file containing initial coordinates with headers id, x, y, and, z
--seed Seed for random number generation for initial node position timestamp
--barnesHutSplits Rounds of splits to use for Barnes-Hut tree building. Number of regions after splitting is 4^barnesHutSplits for 2D and 8^barnesHutSplits for 3D
--barnesHutTheta Theta of the Barnes Hut optimization 1.2
--barnesHutUpdateIter Update Barnes-Hut tree every barnesHutUpdateIter iterations 1
--updateCenter Update Barnes-Hut region centers when not rebuilding Barnes-Hut tree false
--jitterTolerance How much swinging you allow. Above 1 discouraged. Lower gives less speed and more precision. 1.0
--linLogMode Switch ForceAtlas' model from lin-lin to lin-log (tribute to Andreas Noack). Makes clusters more tight. false
--scalingRatio How much repulsion you want. More makes a more sparse graph 2.0 if # nodes >= 100, otherwise 10.0
--gravity Attracts nodes to the center 1.0
--strongGravityMode A stronger gravity law false
--outboundAttractionDistribution Distributes attraction along outbound edges. Hubs attract less and thus are pushed to the borders. false

Example Datasets

Gephi example datasets