Plot methylation beta value distributions

Produces a density plot of methylation beta values (0–1) for each sample in a commaData object. Useful for QC and for comparing methylation level distributions across samples and modification types.

Usage

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

Arguments

object

A commaData object.

mod_type

Character string specifying a single modification type to plot (e.g., "6mA", "5mC"). If NULL (default), all modification types are included and the plot is faceted by mod_type.

per_sample

Logical. If TRUE (default), a separate density curve is drawn for each sample. If FALSE, a single aggregate density curve is drawn per modification type.

Value

A ggplot object. The x-axis shows beta values (0 = unmethylated, 1 = fully methylated); the y-axis shows kernel density. When per_sample = TRUE, curves are colored by sample_name. When multiple modification types are present (and mod_type = NULL), the plot is faceted by mod_type. Sites with NA beta values (below coverage threshold) are silently excluded.

See also

methylomeSummary, plot_coverage

Examples

data(comma_example_data)
plot_methylation_distribution(comma_example_data)


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


# Aggregate across samples
plot_methylation_distribution(comma_example_data, per_sample = FALSE)