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fix ep.tl.umap when neighbors_key is not None #790
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@VladimirShitov if you want to quickly review (or particularly if you have a dev install of ehrapy, confirm this branch now works as it should for you), much appreciated :) else I'll bug Lukas ;) |
@eroell does scanpy suggest to run scanpy neighbors or just calculate neighbors in general? This is legacy code to suggest people to calculate neighbors using the ehrapy API |
I don't have dev install, but the test case from the issue works with scanpy so should be fine now |
Co-authored-by: Lukas Heumos <[email protected]>
you're right ofc it instructs to use |
PR Checklist
docs
is updatedDescription of changes
Fix a bug blocking the native the use of
ep.tl.umap
whenep.pp.neighbors(adata, key_added=<custom>)
.Technical details
Simply remove a faulty check & let scanpy handle it.
Adding tests for plotting and the way to there are an open issue #666, and will be added another time more comprehensively,
Additional context