PeakPlot function

Plot peaks in a genomic region

Display the genomic ranges in a ChromatinAssay object that fall in a given genomic region

PeakPlot(
  object,
  region,
  assay = NULL,
  peaks = NULL,
  group.by = NULL,
  color = "dimgrey",
  sep = c("-", "-"),
  extend.upstream = 0,
  extend.downstream = 0
)

Arguments

• object: A Seurat object
• region: A genomic region to plot
• assay: Name of assay to use. If NULL, use the default assay.
• peaks: A GRanges object containing peak coordinates. If NULL, use coordinates stored in the Seurat object.
• group.by: Name of variable in feature metadata (if using ranges in the Seurat object) or genomic ranges metadata (if using supplied ranges) to color ranges by. If NULL, do not color by any metadata variable.
• color: Color to use. If group.by is not NULL, this can be a custom color scale (see examples).
• sep: Separators to use for strings encoding genomic coordinates. First element is used to separate the chromosome from the coordinates, second element is used to separate the start from end coordinate.
• extend.upstream: Number of bases to extend the region upstream.
• extend.downstream: Number of bases to extend the region downstream.

Returns

Returns a ggplot object

Examples

# plot peaks in assay
PeakPlot(atac_small, region = "chr1-710000-715000")

# manually set color
PeakPlot(atac_small, region = "chr1-710000-715000", color = "red")

# color by a variable in the feature metadata
PeakPlot(atac_small, region = "chr1-710000-715000", group.by = "count")