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
Name of one or more meta.data columns to group (color) cells by.
- palette
Color palette name. Available palettes can be found in thisplot::show_palettes. Default is
"Chinese".- palcolor
Custom colors used to create a color palette. Default is
NULL.- 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.