AutoLayout

[sanast22]

Could you explain how to use the locked_nodes parameter (and other parameters the user can change) in the autolayout function?

[adelhpour]

autolayout Function Parameters

The autolayout function accepts the following parameters:

• max_num_connected_edges (default: 3):

  • An integer that specifies the maximum number of edges (SpeciesReferences) allowed to connect to a node (Species).
  • If a node is connected to more edges than max_num_connected_edges, the autolayout algorithm creates additional alias nodes to represent the species in different reactions.
  • For example, if a species is involved in 5 reactions and max_num_connected_edges is set to 3, the algorithm will generate two SpeciesGlyphs: the first will be associated with the first 3 reactions, and the second with the remaining 2 reactions.

• reset_locked_nodes (default: False):

  • A boolean that determines whether to reset the positions of nodes that were previously locked.
  • If set to True, all existing locked nodes will be unlocked, and only the nodes specified in locked_nodes will be locked in the new layout.
  • If set to False, the positions of previously locked nodes will be preserved while the layout algorithm is applied to the rest.

• locked_nodes (default: []):

  • A list of node IDs whose positions should remain fixed during the autolayout process.
  • Nodes in this list will not be moved, while other nodes will be repositioned according to the layout algorithm.

[sanast22]

For the locked_nodes parameter, are the node IDs the same as speciesIDs?

[adelhpour]

Yup! You need to pass the species ids as locked_nodes.

[adelhpour]

New Feature in v0.3.1: Locking Alias Nodes

In this release, we introduced the ability to lock alias nodes. The locked_nodes parameter can now be one of the following:

1. A list of lists, where each sublist includes:

   • id (string): The ID of the node that must not be moved when the autolayout algorithm is applied.
   • index (integer): The index of the graphical nth graphical object associated to the node that must remain stationary when the autolayout algorithm is applied.

2. A list of node IDs (strings) that must be locked when the autolayout algorithm is applied.