`ExperimentAxisQuery._read()` and `ExperimentAxisQuery.to_anndata()` should read and export, respectively, `obsm` `varm` `obsp` and `varp`.

single-cell-data / SOMA

A flexible and extensible API for annotated 2D matrix data stored in multiple underlying formats.

MIT License

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`ExperimentAxisQuery._read()` and `ExperimentAxisQuery.to_anndata()` should read and export, respectively, `obsm` `varm` `obsp` and `varp`. #177

Closed pablo-gar closed 6 months ago

pablo-gar commented 9 months ago

Currently if a SOMA Experiment has arrays in obsm varm obsp and varp they are not read by ExperimentAxisQuery._read() and thus not exported by ExperimentAxisQuery.to_anndata().

These arrays should be able to be exported to an AnnData via ExperimentAxisQuery.to_anndata().

This ticket doesn't cover the inclusion of the methods .obsm() obsp() varm and varp()

johnkerl commented 7 months ago

@ebezzi does this include both https://github.com/single-cell-data/SOMA/pull/178 and https://github.com/single-cell-data/SOMA/pull/179?