Seurat (version 5.0.3)

CollapseEmbeddingOutliers: 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_"
)

Value

Returns a DimReduc object with the modified embeddings

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

Examples

if (FALSE) {
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")
}