Anndata r #1
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Anndata r #1
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lazappi
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Nov 18, 2025
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| # Read in the remaining layers | ||
| layers <- if (length(X_layers) > 1) { |
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Might want to mention above that the first layer is stored as X
| #' \item `varp` matrices are written out as [`SOMASparseNDArray`] objects | ||
| #' within the measurement's varp group. | ||
| #' } | ||
| #' Expression matrices are transposed (cells as rows) prior to writing. |
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Aren't they already stored this way in the AnnData or am I confused?
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Issue and/or context:
Now that anndataR is released at Bioconductor, we can add it to a dependency to the tiledbsoma r package so data can be read as a native AnnData object without being forced to use Seurat or SingleCellExperiment if it is not necessary.
Changes:
to_anndata(...)to convert a tiledbsoma object to an AnnData objectwrite_soma.AbstractAnnData(...)to convert an AnnData object to a tiledbsoma objectNotes for Reviewer:
to_anndata(...)function could use an argumentas = c("InMemoryAnnData", "HDF5AnnData", "ReticulateAnnData"), ...to allow the user to specify which anndataR backend is used to create the AnnData object, and pass any additional parameter (e.g. path for HDF5AnnData)to_anndata(...)function currently reads everything in memory and then passes it to anndataR::AnnData -- we could move this logic such that first the AnnData object is created with just the obs and var, and other slots are then added to the AnnData to allow for better memory management.