Slingshot curves look weird about slingshot HOT 2 CLOSED

Hi @madhu-coder,

I'm not sure how much I'll be able to help, since it seems like you are adapting code that was adapted from mine, but I might be able to point you in the right direction.

First of all, the slingshot package can handle soft clustering. The SOUPR authors may have been working from an older version (it looks like their repo hasn't been updated in a few years), but this is something that has been supported for a while.

Also, the matrices of points along the curve (ie. curve$s) should have the same dimensionality as your reduced dimensional space. So if you are using the top 3 PCs, then curve$s should only have 3 dimensions, not 257. Again, I'm not really sure what's going on here, because all of this code is from a separate package, but that seems like a pretty big issue.

I would encourage you to re-try your analysis with the functions provided by slingshot, using your membership matrix for the clusterLabels argument. I think it may simplify your workflow and it will definitely make it easier for me to diagnose any problems.

Best,
Kelly

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Hey @kstreet13!
Thank you so much for your guidance!
I have decided to leave that script altogether since even the paper's authors seem to have forgotten about it and are of no help I'm afraid. Thankfully, I found the help here and have used slingshot with the membership matrix as you suggested and I am getting the results. but I need to tweak the number of Principal components used to refine the result. I will come back again in case I come across some error.

Thanks once again!

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