Multithreaded Gephi Force Atlas2 Layout in 2 or 3-d
- 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
Download gephi-toolkit-0.9.2-all.jar and forceatlas2.jar from https://github.com/klarman-cell-observatory/forceatlas2/releases
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 |