Coverage track plot for ATAC data — CoverageTrackPlot • scop

Thin wrapper around Signac::CoveragePlot with scop defaults.

Usage

CoverageTrackPlot(
  srt,
  region,
  assay = NULL,
  group.by = NULL,
  palette = "Chinese",
  palcolor = NULL,
  extend.upstream = 1000,
  extend.downstream = 1000,
  annotation = TRUE,
  peaks = TRUE,
  links = FALSE,
  tile = FALSE,
  ranges = NULL,
  ranges.group.by = NULL,
  region.highlight = NULL,
  verbose = TRUE,
  ...
)

Arguments

srt: A Seurat object.
region: Genomic region passed to Signac::CoveragePlot.
assay: ATAC assay used for plotting.
group.by: Metadata column(s) used to color cells.
palette, palcolor: Palette name (thisplot::show_palettes) or custom colors.
extend.upstream, extend.downstream: Distance to extend around the region.
annotation, peaks, links: Whether to show gene annotation, peaks and links.
tile: Whether to show fragment tiles in the coverage plot.
ranges: Optional genomic ranges added as external tracks.
ranges.group.by: Optional grouping variable used for ranges.
region.highlight: Optional genomic ranges highlighted in the locus panel.
verbose: Whether to print progress messages.
...: Additional parameters passed to Signac::CoveragePlot.

Value

A coverage plot object.

Examples

data("pbmcmultiome_sub", package = "scop")
# Coverage plotting requires an ATAC object with valid fragment information.
if (length(Signac::Fragments(pbmcmultiome_sub[["peaks"]])) > 0) {
  CoverageTrackPlot(
    pbmcmultiome_sub,
    region = rownames(pbmcmultiome_sub[["peaks"]])[1],
    assay = "peaks",
    group.by = "CellType"
  )
}