CollapseEmbeddingOutliers: Move outliers towards center on dimension reduction plot

In Seurat: Tools for Single Cell Genomics

Move outliers towards center on dimension reduction plot

Description

Move outliers towards center on dimension reduction plot

Usage

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

## Not run: 
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")

## End(Not run)

Seurat documentation built on June 8, 2025, 12:24 p.m.