Calculate UMAP projections for coembedding of cells and features

Source: R/CoFAST.R

Calculate UMAP projections for coembedding of cells and features

coembedding_umap(
  seu,
  reduction,
  reduction.name,
  gene.set = NULL,
  slot = "data",
  assay = "RNA",
  seed = 1
)

Arguments

seu

a Seurat object with coembedding in the reductions slot wiht component name reduction.

reduction

a string, specify the reduction component that denotes coembedding.

reduction.name

a string, specify the reduction name for the obtained UMAP projection.

gene.set

a string vector, specify the features (genes) in calculating the UMAP projection, default as all features.

slot

an optional string, specify the slot in the assay, default as `data`.

assay

an optional string, specify the assay name in the Seurat object when adding the UMAP projection.

seed

an optional integer, specify the random seed for reproducibility.

Value

return a revised Seurat object by adding a new reduction component named `reduction.name`.

Details

None

References

None

See also

None

Examples

data(pbmc3k_subset)
data(top5_signatures)
# \donttest{
pbmc3k_subset <- coembedding_umap(
  pbmc3k_subset, reduction = "ncfm", reduction.name = "UMAPsig",
  gene.set = top5_signatures$gene
)
# }