Plot coverage depth distribution

Produces a histogram of sequencing depth (coverage) across sites for each sample in a commaData object. Useful for QC to assess whether coverage is sufficient and consistent across samples.

Usage

plot_coverage(object, mod_type = NULL, per_sample = TRUE)

Arguments

object

A commaData object.

mod_type

Character string specifying a single modification type (e.g., "6mA", "5mC"). If NULL (default), all sites from all modification types are included.

per_sample

Logical. If TRUE (default), the plot is faceted by sample, producing one histogram panel per sample. If FALSE, all samples are overlaid on a single plot with per-sample colors.

Value

A ggplot object. The x-axis shows coverage depth on a log10 scale; the y-axis shows the number of sites at each depth. A vertical dashed line marks the median coverage per sample (when per_sample = TRUE) or across all samples (when per_sample = FALSE). Sites with NA coverage are silently excluded.

See also

coverageDepth, varianceByDepth, plot_methylation_distribution

Examples

data(comma_example_data)
plot_coverage(comma_example_data)


# Overlay all samples on one plot
plot_coverage(comma_example_data, per_sample = FALSE)


# One modification type only
plot_coverage(comma_example_data, mod_type = "6mA")