PersistentHomologyOnGraphs

A visualization tool for using persistent homology to interact with undirected graphs.

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Publication

Persistent Homology Guided Force-Directed Graph Layouts

Ashley Suh, Mustafa Hajij, Bei Wang, Carlos Scheidegger, Paul Rosen

Transactions on Visualization and Computer Graphics (InfoVis 2019), Jan 2020

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Required Software

• Processing 3.x - https://processing.org/download/

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How to run

• Our software is located in PHFDL0D

• Our datasets are located in PHFDL0D/data

• Our layouts generated for figures are located in PHFDL0D/data/paper_layouts

• Run PHFDL0D in Processing and select one of the datasets provided:

  • 6ary.json
  • airport.json
  • barbell.json
  • bcsstk.json
  • caltech.json
  • collab.science.json
  • lobster.json
  • map.science.json
  • miserables.json
  • smith.json
  • train.json
  • us.senate.2007.antivote.json
  • us.senate.2007.covote.json
  • us.senate.2008.antivote.json
  • us.senate.2008.covote.json

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Interaction

All conventional FDL interactions are used (i.e., click and drag nodes etc.)

The persistence barcode on the left has three interactions:

• The filter slider on the top can be moved to the right (to add contracting forces) or to the left (to remove contracting forces). Starting position has no contracting forces added.
• Selecting a bar by left-clicking it will add repulsive forces. Select any bars to add a repulsive force, or unselect to remove the force.
• For larger graphs, a hyperbolic zoom will appear. The zoom position can be adjusted by clicking and dragging or using a scroll wheel.

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Parameters

An interface in the bottom right of has several parameter options. All parameters have been pre-optimized for per layout, so they do not require any further fine tuning.

Toggle the control window by pressing 'c'.

• Standard Force Parameters: adjusts conventional forces
• 0D PH Force Parameters: adjusts PH forces applied to bars that are contracted (spring constant) and repulsed (coulomb constant)
• Drawing Parameters: adjusts sizes of nodes and edges
• Colormap: coloring based on group IDs, specific to datasets
• Reset Positions: resets the layout to a random layout
• Save Data: (over)writes to original JSON file to save adjusted parameters

** Warning: If spring forces are turned up higher, you may need to proportionally lower the timestep to avoid issues within the force-directed layout **