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theislab / cellrank_notebooks

Tutorials and examples for CellRank.
https://cellrank.org
BSD 3-Clause "New" or "Revised" License
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Add directed PAGA to basic tutorial #23

Closed michalk8 closed 4 years ago

michalk8 commented 4 years ago

@Marius1311 could you please take a look at this? closes #https://github.com/theislab/cellrank/issues/344

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michalk8 commented 4 years ago

Closing in favor of #24

Marius1311 commented 4 years ago

Thanks for implementing! The directed PAGA doesn't look right, one edge to epsilon is missing, please compare with the image I posted in https://github.com/theislab/cellrank/issues/344.

I can also tell you why that happens: it's because you use mode="connectivities" when you re-compute the velocity graph in line 7. As we discussed in our call, you don't need to recompute the velocity graph any more and we should remove this from the tutorial, together with the sentence: "Before we start, we recompute the velocity graph using mode_neighbors='connectivities', which ensures that the resulting Markov chain is irreducible."