[r] Add initial support for ragged array writing for Seurat v5 #2523
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Seurat v5 adds support for ragged arrays, where not every `X` layer has exactly the same cells and features. To handle these ragged arrays on ingestion, re-indexing the soma join IDs is necessary to pad the `X` layer to the full domain of the SOMA measurement Implemented SOMA methods: - `write_soma.Assay5()`: write a Seurat v5 assay to a SOMA measurement. When writing `X` layers, if a layer is ragged: - cast layer to `TsparseMatrix` for COO representation - re-index Seurat's character IDs to SOMA join IDs - re-index COO coordinates to SOMA join IDs - write array using `SOMASparseNDArray$private$.write_coo_dataframe()` Notes: - This PR does not implement alternate matrix (eg. DelayedArray, BPCells) ingestion
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Seurat v5 adds support for ragged arrays, where not every
Xlayer has exactly the same cells and features. To handle these ragged arrays on ingestion, re-indexing the soma join IDs is necessary to pad theXlayer to the full domain of the SOMA measurementImplemented SOMA methods:
write_soma.Assay5(): write a Seurat v5 assay to a SOMA measurement. When writingXlayers, if a layer is ragged:TsparseMatrixfor COO representationSOMASparseNDArray$private$.write_coo_dataframe()Notes:
resolves #2658