ExpressionPlot {Signac}

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")