Add Peak Annotation to Coverage Plot.

Add Peak Annotation to Coverage Plot.

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

Arguments

bed.file	The path to consensus peaks file. Default: NULL.
peak.df	The dataframe contains consensus peaks. Default: NULL.
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)