Add Seurat components - #77
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lazappi
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Aug 26, 2025
mumichae
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Aug 29, 2025
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# Conflicts: # CHANGELOG.md
…orkflow Follow the Seurat v5 integration vignette: split the RNA assay into one layer per batch, ScaleData + RunPCA, then IntegrateLayers with CCAIntegration / RPCAIntegration and return the corrected reduction as X_emb. This replaces the v4 SplitObject / FindIntegrationAnchors / IntegrateData path and drops the UMAP that was previously exported as the embedding. Also: - convert dgRMatrix to dgCMatrix sparse-to-sparse instead of via a dense copy - stop loading the counts layer in seurat_rpca; it was unused - forward --dims/--k_anchor/--k_filter/--k_score only when set so Seurat's own defaults apply (k.filter is NA in v5, not 200) - drop the unused X_pca reduction in seurat_rpca
read_h5ad() + as_Seurat() with layers_mapping = c(data = "normalized") builds the Seurat object directly from the h5ad, replacing the manual transpose / sparse conversion / CreateSeuratObject / drop-counts block. Also cite the Seurat v4 paper for seurat_rpca, where RPCA integration was introduced.
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Merging this already so it can be included in the next run; please let me know if you'd like to see anything changed. |
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Describe your changes
Adds two Seurat anchor-based integration methods,
methods/seurat_ccaandmethods/seurat_rpca, implemented on the Seurat v5 workflow from https://satijalab.org/seurat/articles/seurat5_integration:split(obj[["RNA"]], f = obj$batch))ScaleData+RunPCAIntegrateLayers(method = CCAIntegration | RPCAIntegration, orig.reduction = "pca")integrated.cca/integrated.rpca) asX_embTwo deliberate deviations from the vignette, so the components use the same input as every other method in the benchmark:
normalizedlayer (log_cp10k, which is Seurat'sLogNormalize) is assigned to thedatalayer instead of callingNormalizeData()var$hvgis used asVariableFeaturesinstead ofFindVariableFeatures()--dims,--k_anchor,--k_filterand--k_scoreare forwarded only when set, so Seurat's own defaults apply otherwise.Checklist before requesting a review
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Proposed changes are described in the CHANGELOG.md
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