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obs_names and var_names as character/str or not #73
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a strategy following https://anndata.readthedocs.io/en/latest/fileformat-prose.html#dataframe-specification-v0-2-0 might define Perhaps we would implement (on AbstractAnnData) a single-square-brack subset method |
I think it should be possible to support most things by storing names separately. Indexing is maybe only an issue for the in-memory backend anyway, I don't think we want to try to implement indexing on the file-backed backends. Conversion to R objects might be more difficult because as soon as we put things into Maybe @ivirshup can give us an idea of how soon this might happen (and how much we need to worry about it now)? |
It's not imminent. At soonest, my guess would be late this year. But I can ping maintainers of this library ahead of that. |
During the hackathon, I think it was mentioned that
obs_names
andvar_names
might not just be an array of strings, but other dtypes would also be supported. This would cause an issue w.r.t. interoperability in other languages -- at least in R, since standard data frames do not support non-string row names.This has resulted in a somewhat clunky approach to storing obs_names and var_names in an anndataR::AnnData object, since we don't assume we can simply add the obs_names and var_names to any of the slots (X, var, obs, ...) since it will result in a conversion warning being thrown and thus loss of information.
We should figure out what the planned roadmap for this functionality is (probably related to scverse/anndata#777?), and whether there is a different way of resolving this in R because not being to add any dimnames to X and rownames to obs and var is quite cumbersome.
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