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Plot loops

Source: R/trackplots.R
trackplot_loop.Rd

Plot loops

Usage

trackplot_loop(
  loops,
  region,
  color_by = NULL,
  colors = NULL,
  allow_truncated = TRUE,
  curvature = 0.75,
  track_label = "Links",
  return_data = FALSE
)

Arguments

loops

Genomic regions given as GRanges, data.frame, or list. See help("genomic-ranges-like") for details on format and coordinate systems. Required attributes:

  • chr, start, end: genomic position

region

Region to plot, e.g. output from gene_region(). String of format "chr1:100-200", or list/data.frame/GRanges of length 1 specifying chr, start, end. See help("genomic-ranges-like") for details

color_by

Name of a metadata column in loops to use for coloring, or a data vector with same length as loci. Column must be numeric or convertible to a factor.

colors

Vector of hex color codes to use for the color scale. For numeric color_by data, this is passed to ggplot2::scale_color_gradientn(), otherwise it is interpreted as a discrete color palette in ggplot2::scale_color_manual()

allow_truncated

If FALSE, remove any loops that are not fully contained within region

curvature

Curvature value between 0 and 1. 1 is a 180-degree arc, and 0 is flat lines.

return_data

If true, return data from just before plotting rather than a plot.

Value

Plot of loops connecting genomic coordinates

See also

trackplot_combine(), trackplot_coverage(), trackplot_gene(), trackplot_scalebar(), trackplot_genome_annotation()

Examples

peaks <- c(3054877, 3334877, 3534877, 3634877, 3734877)
loops <- tibble::tibble(
  chr = "chr4",
  start = peaks[c(1,1,2,3)],
  end = peaks[c(2,3,4,5)],
  score = c(4,1,3,2)
)
region <- "chr4:3034877-4034877"

## Plot loops
plot <- trackplot_loop(loops, region, color_by = "score")
BPCells:::render_plot_from_storage(plot, width = 6, height = 1.5)