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kstreet13 / slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
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is it possible to set multiple start clusters in slingshot #225

Closed hua1991 closed 7 months ago

hua1991 commented 1 year ago

Hi,

I'm just wondering if is it possible to set multiple start.clus in the slingshot function. Because for t cells, CD4 and CD8 t cells have different differentiation paths. It would make more sense if we could set both naive CD4 and CD8 clusters as start.clus in the slingshot function.

kstreet13 commented 1 year ago

Hi @hua1991,

Good question! This should be possible in settings where you have multiple trajectories, so long as there is only one starting cluster per trajectory. Slingshot can only handle "tree-shaped" trajectories, so complicated topologies with converging and diverging lineages are not supported. Technically, it can handle multiple starting points in the same trajectory if they all have the same endpoint (by setting the endpoint as the beginning and then flipping the pseudotimes), but that's a special case.

In order to get multiple, disconnected trajectories, you can try setting omega = TRUE (and possibly tuning the omega_scale parameter) when you run slingshot.

Best, Kelly