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SCmultiomics Analysis in LongCOVID

13 RNA Batch Assessment

13.1 By sample 

DefaultAssay(combined) <- "RNA"
DimPlot(combined, reduction = "umap.rna_regressedRibo", group.by = "sample") +
  ggtitle("RNA UMAP — by sample")

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13.2 By donor 

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

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13.3 By sample and donor 

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

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13.4 By condition 

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

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13.5 Split by sample

Splitting by sample reveals whether the cluster structure is consistent across samples — clusters that appear in only one sample are likely sample-specific artefacts rather than true cell types.

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

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