Highlight regions along sequence arcs — geom_seq

Draws rectangular bands on sequence arcs for one or more coordinate intervals. This is useful for marking loci, repeats, CRISPR arrays, or other user-defined regions without turning them into gene arrows.

Usage

geom_seq_region(
  mapping = NULL,
  data = NULL,
  regions = NULL,
  region_fill = "#F59E0B",
  region_color = "#B45309",
  region_alpha = 0.25,
  region_width = 0.08,
  region_offset = 0,
  region_side = c("inside", "outside", "auto"),
  show_legend = FALSE,
  ...
)

Arguments

mapping: Default NULL (uses pre-computed data)
data: Optional data.frame; an alias for regions when regions is NULL.
regions: data.frame with at least seq_id, start, end; optional label, category and color.
region_fill: Character. Default fill colour for regions, default "#F59E0B".
region_color: Character. Outline colour, default "#B45309".
region_alpha: Numeric (0-1). Region alpha, default 0.25.
region_width: Numeric. Band width in chord radius units, default 0.08.
region_offset: Numeric. Radial offset from the sequence arc, default 0.
region_side: Character. "inside", "outside" or "auto"; "auto" places regions inside the chord when possible.
show_legend: Logical. Whether to show a legend for category colours, default FALSE.
...: Additional arguments passed to geom_polygon()

Value

A list of ggplot2 layers

Examples

library(ggchord)
data(seq_data_example)
regions <- data.frame(seq_id = "MT108731.1",
                      start = 1000, end = 4000,
                      color = "orange")
p <- ggchord(seq_data_example) + geom_seq() + geom_seq_region(regions)
p