Move outliers towards center on dimension reduction plot

Move outliers towards center on dimension reduction plot

CollapseEmbeddingOutliers(
  object,
  reduction = "umap",
  dims = 1:2,
  group.by = "ident",
  outlier.sd = 2,
  reduction.key = "UMAP_"
)

Arguments

object

Seurat object

reduction

Name of DimReduc to adjust

dims

Dimensions to visualize

group.by

Group (color) cells in different ways (for example, orig.ident)

outlier.sd

Controls the outlier distance

reduction.key

Key for DimReduc that is returned

Value

Returns a DimReduc object with the modified embeddings

Examples

if (FALSE) { # \dontrun{
data("pbmc_small")
pbmc_small <- FindClusters(pbmc_small, resolution = 1.1)
pbmc_small <- RunUMAP(pbmc_small, dims = 1:5)
DimPlot(pbmc_small, reduction = "umap")
pbmc_small[["umap_new"]] <- CollapseEmbeddingOutliers(pbmc_small,
    reduction = "umap", reduction.key = 'umap_', outlier.sd = 0.5)
DimPlot(pbmc_small, reduction = "umap_new")
} # }