geom_peak: Add Peak Annotation to Coverage Plot.

In ggcoverage: Visualize Genome Coverage with Various Annotations

Add Peak Annotation to Coverage Plot.

Description

Add Peak Annotation to Coverage Plot.

Usage

geom_peak(
  bed.file,
  peak.color = "black",
  peak.size = 5,
  plot.space = 0.1,
  plot.height = 0.1
)

Arguments

bed.file	The path to bed file.
peak.color	Peak color. Default: black.
peak.size	The line size of peak. Default: 5.
plot.space	Top and bottom margin. Default: 0.1.
plot.height	The relative height of peak annotation to coverage plot. Default: 0.2.

Value

Plot.

Examples

library(ggcoverage)
library(rtracklayer)
sample.meta <- data.frame(
  SampleName = c("Chr18_MCF7_ER_1", "Chr18_MCF7_ER_2", "Chr18_MCF7_ER_3", "Chr18_MCF7_input"),
  Type = c("MCF7_ER_1", "MCF7_ER_2", "MCF7_ER_3", "MCF7_input"),
  Group = c("IP", "IP", "IP", "Input")
)
# track folder
track.folder <- system.file("extdata", "ChIP-seq", package = "ggcoverage")
# load bigwig file
track.df <- LoadTrackFile(
  track.folder = track.folder, format = "bw",
  meta.info = sample.meta
)
gtf.file <- system.file("extdata", "used_hg19.gtf", package = "ggcoverage")
gtf.gr <- rtracklayer::import.gff(con = gtf.file, format = "gtf")
# create mark region
mark.region <- data.frame(start = c(76822533), end = c(76823743), label = c("Promoter"))
basic.coverage <- ggcoverage(
  data = track.df, color = "auto", region = "chr18:76822285-76900000",
  mark.region = mark.region, show.mark.label = FALSE
)
# get consensus peak file
peak.file <- system.file("extdata", "ChIP-seq", "consensus.peak", package = "ggcoverage")
basic.coverage + geom_gene(gtf.gr = gtf.gr) + geom_peak(bed.file = peak.file)

ggcoverage documentation built on Sept. 6, 2022, 9:06 a.m.