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pinellolab / STREAM

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
http://stream.pinellolab.org
GNU Affero General Public License v3.0
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Attributes interpretation #84

Closed MingBit closed 4 years ago

MingBit commented 4 years ago

Hallo,

Thanks for the great tool! I'm still new to STREAM and doing the first analysis according to this tutorial. Everything works properly so far. Just a little bit confused about the results stored in adata object.

I'm wondering where I could find the documentation for the new attributes (e.g. branch_id, branch_lam, S0_pseudotime) stored in adata object. For instance, I'd like to select cells from one branch (S3 -> S0) and order cell by pseudotime. However, I'm not sure which one should I use?

looks forward to your reply. Thank you.

huidongchen commented 4 years ago

Hi, thanks for trying STREAM. Sorry about the lack of documentation for the attributes.

Re your question, branch_id_alias and S0_pseudotime should suffice in terms of selecting the cells needed.

branch_lam and branch_id are both the 'raw' attributes during the structure learning, which are the lamda, i.e. the arc-length from the beginning of the curve, and the id internally used to label branches, respectively. They are preserved just for the purpose of debugging. You most likely won't need them.

Anyhow, thanks for the feedback. We will keep improving it. Hope the above is helpful to you.

MingBit commented 4 years ago

Yeah! it's really helpful. Thanks a lot! Does it mean that the pseudotime at terminal point is sufficient for ordering? For instance, S2_pseudotime can be used for ordering cells from pathway (S3->S1->S2)?

huidongchen commented 4 years ago

S2_pseudotime means the ordering of all cells when choosing 'S2' as the starting node.

That being said, to order cells along the trajectory (S3->S1->S2), you should consider S3_pseudotime. Also you might want to only keep the cells assigned to that path by choosing the cells from branch ('S3','S1') and ('S1','S2')

MingBit commented 4 years ago

Score! Thank you so much! :+1: