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 $to_seurat_assay() to share code with v3 assay outgestion
Seurat v5 adds support for ragged arrays, where not every
Xlayer has exactly the same cells and features. To handle this, raggedXlayers need to be re-indexed and re-shaped on ingestion to resize down to only the data presentModified SOMA methods:
SOMAExperimentAxisQuery$to_seurat()andSOMAExperimentAxisQuery$to_seurat_assay(): now read in as v5 assaysNew SOMA methods:
SOMAExperimentAxisQuery$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 outgestionRequires #2523 and #3007
SC-52261