Signac: ExpressionPlot – R documentation

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ExpressionPlot

Plot gene expression

Description

Display gene expression values for different groups of cells and different genes. Genes will be arranged on the x-axis and different groups stacked on the y-axis, with expression value distribution for each group shown as a violin plot. This is designed to work alongside a genomic coverage track, and the plot will be able to be aligned with coverage tracks for the same groups of cells.

Usage

ExpressionPlot(
  object,
  features,
  assay = NULL,
  group.by = NULL,
  idents = NULL,
  slot = "data"
)

Arguments

`object`	A Seurat object
`features`	A list of features to plot
`assay`	Name of the assay storing expression information
`group.by`	A grouping variable to group cells by. If NULL, use the current cell identities
`idents`	A list of identities to include in the plot. If NULL, include all identities
`slot`	Which slot to pull expression data from

Examples

ExpressionPlot(atac_small, features = "TSPAN6", assay = "RNA")

Signac

Analysis of Single-Cell Chromatin Data

v1.2.1

MIT + file LICENSE

Authors

Tim Stuart [aut, cre] (<https://orcid.org/0000-0002-3044-0897>), Avi Srivastava [aut] (<https://orcid.org/0000-0001-9798-2079>), Paul Hoffman [ctb] (<https://orcid.org/0000-0002-7693-8957>), Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)

Initial release

2021-05-11