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[FEAT]: More grid-like graph layout for the model diagram #5823

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liunelson opened this issue Dec 12, 2024 · 0 comments
Open

[FEAT]: More grid-like graph layout for the model diagram #5823

liunelson opened this issue Dec 12, 2024 · 0 comments
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@liunelson
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liunelson commented Dec 12, 2024

Is your feature request related to a problem? Please describe.
We've received some comments from users (particularly the UCSD team) about how the model diagrams are

  • hard to read because of the swooping/looping edges
  • emphasis on the transition nodes over the states
  • hard to compare with diagrams in paper for validation since papers tend to use different layouts (grid-like)

In the case of the Zombie model:

  • currently
    Image
  • proposed
    Image

Describe the solution you'd like

  • Do not use the transition nodes during the layout calculation
  • Toggle the controller edges and rate law expressions (default = off, so users just want to quickly check if the Terarium model matches a paper's model)
  • Pretty-print the SymPy rate law strings
  • Larger arrow heads to make the state-to-state flow pattern more obvious
  • Use hierarchical/Sugiyama layout algorithm to emphasize flow pattern?
@liunelson liunelson added the feature New feature or request label Dec 12, 2024
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