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algorithms:kamada

Kamada-Kawai

Layout algorithm based on a physical spring force system. Each node is connected with all the remaining nodes with a spring, and each spring has a constant and equilibrium length related to the distance in the network between the two nodes. The closer the nodes are in the network, the stronger the spring is and the shorter its equilibrium length. Reaching the equilibrium force requires a very expensive computation, so this layout is only recommended for small networks (~1000 nodes), although it may produce beautiful network disposals.

Parameter Type Default Description
Iterations* int > 0 500 Number of iterations of the plugin.
Initial temperature float > 0 10.0 Proportional to the maximum node displacement allowed in each iteration.
Cooling Factor float ∈ (0,1) 0.990 Reduction factor of the temperature in each iteration. Increase it to allow for large node displacements in the first iterations.
2D Bool False Whether to use a 2D or 3D layout.
Seed int 0 Random seed
Link weight text None Link property that represents the intensity of the attraction between connected nodes. Must have positive values
Reset PositionsBool False Whether to delete any previously calculated positions.

* Required Field

The next two plots are a 2D and 3D layout of a gene network (yeast). Node size corresponds to its degree and its color identifies its community.



References:

  • Kamada, T. and Kawai S., An Algorithm for Drawing General Undirected Graphs, Inf. Process. Lett. 1989.
algorithms/kamada.txt · Last modified: 2018/12/20 14:25 by systems