obs_names and var_names as character/str or not

[rcannood]

During the hackathon, I think it was mentioned that obs_names and var_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.

[mtmorgan]

a strategy following https://anndata.readthedocs.io/en/latest/fileformat-prose.html#dataframe-specification-v0-2-0 might define obs_attrs() and including obs_attrs()[["_name"]] the column name of the index. obs would return a data.frame that included the named column. Is it actually a problem not having row names? This is the norm in the tidyverse world.

Perhaps we would implement (on AbstractAnnData) a single-square-brack subset method ad[cidx, ridx] that created a subset / view based on the corresponding row / column index,.

[lazappi]

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 colnames/rownames they will coerced to characters.

Maybe @ivirshup can give us an idea of how soon this might happen (and how much we need to worry about it now)?

[ivirshup]

It's not imminent. At soonest, my guess would be late this year. But I can ping maintainers of this library ahead of that.