Shrinking strength does not work

[yueqiw]

Hi,

First of all, Slingshot is a great package!

In the documentation, the shrink parameter is described as follows:

shrink: logical or numeric between 0 and 1, determines whether and how much to shrink branching lineages toward their average prior to the split.

However, when I try shrink = 0.1, it produces the same result as shrink = TRUE. Looking at the code, I don't see how a numeric shrink is used. Is there another way to set the strength of shrink? Thanks!

[kstreet13]

Thanks!
And thank you very much for pointing this out. You're absolutely right that the shrink parameter was not doing what it says in the documentation. I'm not sure where along the way that functionality was lost, but I just pushed a new update to the develop branch that should restore it (and I will add it to master once it passes the usual checks).

[yueqiw]

Thanks! I made a similar change in my fork. I've also been trying to use RNA velocity to guide the initialization of Slingshot, so that the fitted trajectories are better aligned with RNA velocity vectors. I've got it to work to some extent but I feel that it can be done better. If you're interested, we can discuss it at some point.

[kstreet13]

@yueqiw
Yeah, this sounds very interesting! I'm going to close this issue, but feel free to email me at kstreet@berkeley.edu if you want to discuss it further.

[yueqiw]

@kstreet13 Sure. I'm doing manuscript writing but will email you in the next week or so.