ingest after bbknn produces poor results
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Description
Hi,
I tried ingest using the reference made with BBKNN. As @ivirshup said, ingest was worked by adding adata_ref.uns['neighbors']['params']['metric'] = 'euclidean'. However, the result was quite poor.
In contrast, if I merge all datasets (eg references and query), it worked well, but when we want to take over the reference embedding, I actually want to use ingest rather than run bbknn again. Is there any option to feed in this case? or should I ask this in the BBKNN repo?
This is the notebook can reproduce the problem.
https://nbviewer.jupyter.org/github/yyoshiaki/ingest_after_bbknn/blob/main/notebook.ipynb
https://github.com/yyoshiaki/ingest_after_bbknn/blob/main/notebook.ipynb
Originally posted by @yyoshiaki in https://github.com/theislab/scanpy/issues/1122#issuecomment-838476193
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First steps
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Research direction
Start by running notebook.ipynb from the linked ingest_after_bbknn repository to reproduce the poor ingest result, then inspect how the BBKNN reference and its neighbors parameters are passed to ingest. Done means establishing whether this combination is supported and recording a reproducible fix or limitation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100