KeyError: 'dpt_order_indices' missing if branching=0
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Description
I don't think this is fixed in the previous issue https://github.com/theislab/scanpy/issues/129.
If you run sc.tl.dpt(adata) it creates the dpt_pseudotime property in obs as expected. However using dpt in plotting functions fails like sc.pl.dpt_timeseries(adata). This is due to the dpt_order_indices property not being created if branching=0.
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Research direction
Start by reproducing the issue with sc.tl.dpt(adata) followed by sc.pl.dpt_timeseries(adata), and inspect how branching=0 affects dpt_order_indices. Trace the dpt and dpt_timeseries entry points; done means the plotting call no longer raises KeyError while dpt_pseudotime remains available.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data-visualization
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100