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kstreet13 avatar kstreet13 commented on June 30, 2024 1

Hi @astrid12345,

That's a very good question! You're right that there isn't a Slingshot parameter that directly adjusts this, but you can generally get higher complexity or more branching points by adjusting the cluster labels used by Slingshot. More clusters will lead to more opportunities for branching points, so generally more complex trajectories. For example, if your input clusters were generated by k-means or Louvain clustering, you could try increasing the k or resolution parameters, respectively. Separately, and this might not make much of a difference, but it might be worth switching the distance metric (dist.method) to mnn, so that connections between clusters are based on cells in close proximity rather than overall shape.

Best,
Kelly

from slingshot.

astrid12345 avatar astrid12345 commented on June 30, 2024

Thank you! Those are very helpful suggestions! I will give it a go.

from slingshot.

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