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LouisFaure / scFates

a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.
https://scfates.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
50 stars 2 forks source link

Error in scf.tl.branch_specific #13

Closed min0609 closed 8 months ago

min0609 commented 1 year ago

Hi, First of all, thank you for this wonderful tool.

I was following the tutorial 'Tree analysis', but when I ran the following command line, I got the error message below: scf.tl.branch_specific(adata,root_milestone="follicular1",milestones=["PTC2","ATC1","ATC3", "PTCEO", "BifATC"],effect=2)

image

Could you please suggest me how to solve the problem?

I also would like to know the difference between seg and milestone.

Thank you!

LouisFaure commented 1 year ago

Apologies for the lack of answer, I am currently doing a sabbatical.

A segment is considered as a section of the tree from one tip or fork to another, while milestones designate the actual tips and forks. The latter is easier to use when one want to specify a subset of trajectory to focus on for analysis such as branch DE.

This error tells that it cannot find any data in .uns part of your anndata with the keys of your trifurcation. Have you run test_fork with the same milestones before?

In more details, a cell is given a milestone that is the closest fork or tip in term of pseudotime distance