[r] [WIP] Add support for reading v5 assays from an axis query #3008
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johnkerl
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Nov 7, 2024
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| # Read in layers | ||
| for (lyr in layers) { |
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| for (lyr in layers) { | |
| for (layer_name in layer_names) { |
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Skipping this as the I've applied the lname → layer_name suggestion above. Changing here will overwrite the layer_name variable defined above, and I still need said layer_name (which is why I originally used lname and lyr as it kept the two uses separate)
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 `$to_seurat_assay()` to share code with v3 assay outgestion Requires #2523 and #3007 [SC-52261](https://app.shortcut.com/tiledb-inc/story/52261/)
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[ci skip] Co-authored-by: John Kerl <[email protected]>
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Seurat v5 adds support for ragged arrays, where not every
Xlayer has exactly the same cells and features. To handle this, raggedXlayers need to be re-indexed and re-shaped on ingestion to resize down to only the data presentModified SOMA methods:
SOMAExperimentAxisQuery$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