pyforceatlas2 0.0.4

Fast Gephi's ForceAtlas2 graph layout algorithm written in Python for Python.

PyForceAtlas2

PyForceAtlas2 is a Python implementation of the ForceAtlas2 graph layout algorithm. Originally designed for Gephi, this implementation is optimized for reproducible and high-performance network visualization in Python, supporting both NetworkX and igraph.

Features

• High Performance: Barnes-Hut optimization for large networks.
• Customizable: Fine-tune attraction, repulsion, gravity, and speed parameters.
• Versatile: Seamless integration with NetworkX and igraph.
• Reproducible: Easily set random seeds for deterministic layouts.

Installation

Install PyForceAtlas2 via pip:

pip install pyforceatlas2

Usage Example

The following example demonstrates how to compute a layout for a random geometric graph and visualize it with NetworkX and Matplotlib:

"""
Example: ForceAtlas2 Layout on a Random Geometric Graph
--------------------------------------------------------

This script generates a random geometric graph with 400 nodes,
computes a ForceAtlas2 layout, and visualizes the result.
"""

import random
import networkx as nx
import matplotlib.pyplot as plt
from pyforceatlas2 import ForceAtlas2

# Set a random seed for reproducibility.
random.seed(888)

# Generate a random geometric graph: nodes are connected if they are within radius 0.2.
G = nx.random_geometric_graph(400, 0.2)

# Initialize ForceAtlas2 with custom parameters.
forceatlas2 = ForceAtlas2(
    outbound_attraction_distribution=False,  # Do not dissuade hubs.
    edge_weight_influence=1.0,
    lin_log_mode=True,                       # Use LinLog mode for attraction forces.
    jitter_tolerance=10.0,                     # Tolerance for oscillations.
    barnes_hut_optimize=True,                  # Enable Barnes-Hut optimization.
    barnes_hut_theta=2.2,                      # Trade-off between accuracy and speed.
    scaling_ratio=2.0,                         # Controls overall repulsion strength.
    strong_gravity_mode=False,                 # Use standard gravity.
    gravity=1.0,                               # Gravitational constant.
    verbose=True,
)

# Compute the layout. Returns a dict mapping each node to an (x, y) coordinate.
positions = forceatlas2.forceatlas2_networkx_layout(G, pos=None, iterations=100)

# Visualize the graph.
nx.draw_networkx_nodes(G, positions, node_size=20, node_color="blue", alpha=0.4)
nx.draw_networkx_edges(G, positions, edge_color="green", alpha=0.05)
plt.axis("off")
plt.show()

API Overview

The main entry point is the ForceAtlas2 class:

from pyforceatlas2 import ForceAtlas2

# Initialize with desired parameters.
forceatlas2 = ForceAtlas2(
    outbound_attraction_distribution=False,
    edge_weight_influence=1.0,
    lin_log_mode=True,
    jitter_tolerance=10.0,
    barnes_hut_optimize=True,
    barnes_hut_theta=2.2,
    scaling_ratio=2.0,
    strong_gravity_mode=False,
    gravity=1.0,
    verbose=True,
)

# For a NetworkX graph:
positions = forceatlas2.forceatlas2_networkx_layout(G, pos=None, iterations=100)

# For an igraph graph:
layout_obj = forceatlas2.forceatlas2_igraph_layout(igraph_graph, pos=None, iterations=100)

References

• ForceAtlas2 Paper:
  Jacomy, M., Venturini, T., Heymann, S., & Bastian, M. (2014).
  ForceAtlas2, a continuous graph layout algorithm for handy network visualization designed for the Gephi software.
  PLoS ONE, 9(6), e98679.
  DOI: 10.1371/journal.pone.0098679

Contributing

Contributions, bug reports, and feature requests are welcome! Please open an issue or submit a pull request on GitHub.

License

This project is licensed under the GNU General Public License v3.0 (GPLv3). See the LICENSE file for details.