algorithms:kamada

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algorithms:kamada [2018/10/18 13:41] systems |
algorithms:kamada [2018/12/20 14:25] (current) systems |
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^Parameter ^Type ^Default ^Description ^ | ^Parameter ^Type ^Default ^Description ^ | ||

- | |Iterations |int > 0 |500 |Number of iterations of the plugin.| | + | |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.| | + | |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.| | + | |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.| | + | |2D |Bool |False |Whether to use a 2D or 3D layout.| |

- | |Seed* |int |0 |Random seed| | + | |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| | + | |Link weight |text |None |Link property that represents the intensity of the attraction between connected nodes. Must have positive values| |

- | |Reset Positions*|Bool |False |Whether to delete any previously calculated positions.| | + | |Reset Positions|Bool |False |Whether to delete any previously calculated positions.| |

- | * //Advanced Configuration Parameter// | + | * //Required Field// |

The next two plots are a 2D and 3D layout of a gene network (yeast). Node size corresponds to its [[Algorithms:Degree|degree]] and its color identifies its [[Algorithms:Communities_Louvain|community]]. | The next two plots are a 2D and 3D layout of a gene network (yeast). Node size corresponds to its [[Algorithms:Degree|degree]] and its color identifies its [[Algorithms:Communities_Louvain|community]]. |

algorithms/kamada.txt · Last modified: 2018/12/20 14:25 by systems