ExpressionPlot: Plot gene expression

In Signac: Analysis of Single-Cell Chromatin Data

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 documentation built on Sept. 11, 2024, 9:30 p.m.