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SCmultiomics Analysis in PASC

15 ATAC Batch Assessment

15.1 By sample 

DimPlot(combined, reduction = "umap.atac", group.by = "sample") +
  ggtitle("ATAC UMAP — by sample")

15.2 By donor 

DimPlot(combined, reduction = "umap.atac", group.by = "donor_id") +
  ggtitle("ATAC UMAP — by donor")

15.3 By sample and donor 

DimPlot(combined, reduction = "umap.atac", group.by = "sample_donor") +
  ggtitle("ATAC UMAP — by sample-donor")

15.4 By condition 

DimPlot(combined, reduction = "umap.atac", group.by = "individual_condition") +
  ggtitle("ATAC UMAP — by condition")

15.5 Split by sample 

DimPlot(combined, reduction = "umap.atac",
        split.by = "sample", group.by = "sample_donor") +
  ggtitle("ATAC UMAP — split by sample")

15.6 Summary

If the plots above show strong separation by sample or sample_donor in either modality, batch correction should be applied before building the WNN graph:

  • RNA: addressed in the Integration chapter via Seurat CCA (FindIntegrationAnchors / IntegrateData) using cell-type marker genes as anchors
  • ATAC: if donor/sample separation is evident in the LSI UMAP, Harmony correction on the LSI embedding should be applied: