Skip to contents

Publication-ready visualization toolkit for rendering genomic track data and statistical summaries related to 3D chromatin interactions

Source: R/visualization.R
plot_peaks_interactions.Rd

Generates an integrative genomic track plot resembling IGV, displaying chromatin loops as arcs, loop anchors as rectangles, optional overlapping features (e.g., ChIP-seq peaks), and annotated genes. Loop arcs can be colored or sized by interaction score (7th column in BEDPE).

Usage

plot_peaks_interactions(
  bedpe_file,
  target_bed = NULL,
  chr = NULL,
  from = NULL,
  to = NULL,
  species = "hg38",
  max_levels = 10,
  base_anchor_height = 0.05,
  loop_color = "#5D6D7E",
  anchor_color = "#3498DB",
  overlap_color = "#02ABB4",
  exon_color = "#2C3E50",
  intron_color = "black",
  score_to_alpha = TRUE,
  min_score = NULL,
  save_file = NULL
)

Arguments

bedpe_file

Character. Path to a BEDPE file (at least 6 columns; 7th column used as score if present).

target_bed

Optional character. Path to a BED file (e.g., peaks) to overlay below the loop track.

chr

Character. Chromosome name (e.g., "chr8"). If NULL, inferred from most frequent chromosome in BEDPE.

from

Numeric. Start coordinate of the region to plot.

to

Numeric. End coordinate of the region to plot.

species

Character. Genome assembly: "hg38", "hg19", "mm10", or "mm9".

max_levels

Integer. Maximum number of vertical levels for arc stacking (default: 10).

base_anchor_height

Numeric. Height of anchor rectangles (default: 0.1).

loop_color

Character. Default color for arcs when no score is provided (e.g., "#5D6D7E").

anchor_color

Character. Color for loop anchor rectangles (default: "#3498DB").

overlap_color

Character. Color for overlap track (default: "#E74C3C").

exon_color

Character. Gene exon fill color (default: "#2C3E50").

intron_color

Character. Gene intron line color (default: "black").

score_to_alpha

Logical. Whether to map interaction scores to arc transparency.

min_score

Logical. If TRUE, use score to control arc line width instead of color (not yet implemented in current version; future extension).

save_file

Optional character. File path to save the plot (e.g., "region_plot.pdf").

Value

A ggplot object.

Examples

# 1. Get paths to example files included in the package
bedpe_path <- system.file("extdata", "example_loops_1.bedpe", package = "looplook")
bed_path <- system.file("extdata", "example_peaks.bed", package = "looplook")

# 2. Run plotting (requires TxDb package for gene annotation)
if (bedpe_path != "" &&
  requireNamespace("TxDb.Hsapiens.UCSC.hg38.knownGene", quietly = TRUE) &&
  requireNamespace("org.Hs.eg.db", quietly = TRUE)) {
  # Example : Integrative plot with overlapping peaks and output to file
  p2 <- plot_peaks_interactions(
    bedpe_file = bedpe_path,
    target_bed = bed_path,
    chr = "chr1",
    from = 11884299,
    to = 12106581,
    species = "hg38",
    save_file = tempfile(fileext = ".pdf")
  )
}
#>   2169 genes were dropped because they have exons located on both strands of
#>   the same reference sequence or on more than one reference sequence, so cannot
#>   be represented by a single genomic range.
#>   Use 'single.strand.genes.only=FALSE' to get all the genes in a GRangesList
#>   object, or use suppressMessages() to suppress this message.
#> 'select()' returned 1:1 mapping between keys and columns
#> 'select()' returned 1:1 mapping between keys and columns
#> Warning: The `size` argument of `element_rect()` is deprecated as of ggplot2 3.4.0.
#> ℹ Please use the `linewidth` argument instead.
#> ℹ The deprecated feature was likely used in the looplook package.
#>   Please report the issue at <https://github.com/zying106/looplook/issues>.