[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 this, ragged `X` layers need to be re-indexed and re-shaped on ingestion to resize down to only the data present Modified SOMA methods: - `SOMAExperimentAxisQuery$to_seurat()` and `SOMAExperimentAxisQuery$to_seurat_assay()`: now read in as v5 assays New SOMA methods: - `SOMAExperimentAxisQuery$private$.to_seurat_assay_v5()`: helper method to read in ragged and non-ragged arrays into a v5 assay; note this method only handles expression layers, all other assay-level information is handled by parent `$to_seurat_assay()` to share code with v3 assay outgestion Requires #2523 and #3007 [SC-52261](https://app.shortcut.com/tiledb-inc/story/52261/)
Seurat v5 adds support for ragged arrays, where not every `X` layer has exactly the same cells and features. To handle these ragged arrays on ingestion, re-indexing the soma join IDs is necessary to pad the `X` layer to the full domain of the SOMA measurement Implemented SOMA methods: - `write_soma.Assay5()`: write a Seurat v5 assay to a SOMA measurement. When writing `X` layers, if a layer is ragged: - cast layer to `TsparseMatrix` for COO representation - re-index Seurat's character IDs to SOMA join IDs - re-index COO coordinates to SOMA join IDs - write array using `SOMASparseNDArray$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:
SC-46644
resolves #2658