Plot gene expression — ExpressionPlot • Signac

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,
  layer = "data",
  slot = deprecated()
)

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
layer: Name of layer to pull expression data from
slot: Which slot to pull expression data from

Examples

# \donttest{
ExpressionPlot(atac_small, features = "ASMTL", assay = "RNA")

# }