Fix the number of lineage

[jakyzhu]

Hi, so I have a single cell data and I do know there is only one possible directed linear lineage. Is there anyway that I can fix the lineage number in the slingshot? Thanks,

[kstreet13]

Hey @jakyzhu ,

Yes, there are ways to do this, but only for the specific case of one lineage. The easiest approach would probably be to run slingshot without providing any cluster labels. This will always lead to a single lineage being identified and the curve representing that lineage will be essentially the same as what you would get from fitting a principal curve. Similarly, you could cluster into k = 2 clusters and still be guaranteed only one lineage, but here you would have control over the directionality (via start.clus).

Beyond the single-lineage case, there is no simple way to guarantee a specific number of lineages. We recommend using the end.clus argument to specify known endpoint clusters, instead.

[jakyzhu]

@kstreet13 Oh, thanks for the quick reply:) It helps a lot