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R
Seurat

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_"
)

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

Tools for Single Cell Genomics

v4.0.1
GPL-3 | file LICENSE
Authors
Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]
Initial release
2021-03-17

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