Seurat: VizDimLoadings – R documentation

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Seurat

VizDimLoadings

Visualize Dimensional Reduction genes

Description

Visualize top genes associated with reduction components

Usage

VizDimLoadings(
  object,
  dims = 1:5,
  nfeatures = 30,
  col = "blue",
  reduction = "pca",
  projected = FALSE,
  balanced = FALSE,
  ncol = NULL,
  combine = TRUE
)

Arguments

`object`	Seurat object
`dims`	Number of dimensions to display
`nfeatures`	Number of genes to display
`col`	Color of points to use
`reduction`	Reduction technique to visualize results for
`projected`	Use reduction values for full dataset (i.e. projected dimensional reduction values)
`balanced`	Return an equal number of genes with + and - scores. If FALSE (default), returns the top genes ranked by the scores absolute values
`ncol`	Number of columns to display
`combine`	Combine plots into a single `patchworked` ggplot object. If `FALSE`, return a list of ggplot objects

Value

A patchworked ggplot object if combine = TRUE; otherwise, a list of ggplot objects

Examples

data("pbmc_small")
VizDimLoadings(object = pbmc_small)

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

VizDimLoadings

Description

Usage

Arguments

Value

Examples

Seurat

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