Genome browser–style methylation track plot

Plots methylation beta values for individual sites along a chromosome region in a genome browser–style layout, with one panel per sample. Optionally overlays genomic feature annotations as colored rectangles in a separate track below the methylation data.

Usage

plot_genome_track(
  object,
  chromosome,
  start = NULL,
  end = NULL,
  mod_type = NULL,
  annotation = NULL
)

Arguments

object

A commaData object.

chromosome

Character string. The chromosome (sequence name) to plot. Must be present in names(genome(object)).

start

Integer or NULL. Start position of the region to display (1-based, inclusive). If NULL, the plot begins at position 1.

end

Integer or NULL. End position of the region to display (1-based, inclusive). If NULL, the plot extends to the end of the chromosome.

mod_type

Character string specifying a single modification type to display (e.g., "6mA", "5mC"). If NULL (default), all modification types are shown, colored differently.

annotation

A GRanges object of genomic features to display in the annotation track, NULL (default, uses annotation(object) if available), or FALSE to suppress the annotation track entirely.

Value

A ggplot object. The methylation track shows individual sites as points (x = genomic position, y = beta value 0–1) colored by modification type, faceted by sample. If annotation features are present on the selected chromosome (and annotation is not FALSE), they are displayed as colored rectangles in a separate annotation panel below.

See also

annotateSites, plot_metagene

Examples

data(comma_example_data)
plot_genome_track(comma_example_data, chromosome = "chr_sim")


# Restrict to a region
plot_genome_track(comma_example_data, chromosome = "chr_sim",
                  start = 1000, end = 50000)


# One modification type, no annotation
plot_genome_track(comma_example_data, chromosome = "chr_sim",
                  mod_type = "6mA", annotation = FALSE)