Add CNV Annotation to Coverage Plot.

geom_cnv(
  cnv.df,
  bin.col = 3,
  cn.col = 4,
  ref.cn = 2,
  bin.point.color = "grey",
  bin.point.alpha = 0.6,
  cn.line.color = "red",
  ref.line.color = "black",
  plot.space = 0.1,
  plot.height = 0.2
)

Arguments

cnv.df	Dataframe contains copy number information, should contains at least three columns (chr, position, bin value, copy number).
bin.col	Column index for bin value (point). Default: 3.
cn.col	Column index for copy number (line). Default: 4.
ref.cn	Reference copy number (ploidy). Default: 2.
bin.point.color	Point color of bin value. Default: "grey".
bin.point.alpha	Point alpha of bin value. Default: 0.6.
cn.line.color	Line color of copy number. Default: "red".
ref.line.color	Line color of reference copy number (ploidy). Default: "black".
plot.space	Top and bottom margin. Default: 0.1.
plot.height	The relative height of contact map to coverage plot. Default: 0.2.

Value

Plot.

Examples

# library(ggcoverage)
# library(utils)
# library("BSgenome.Hsapiens.UCSC.hg19")
# # prepare files
# cnv.file <- system.file("extdata", "DNA-seq", "SRR054616_copynumber.txt", package = "ggcoverage")
# track.file <- system.file("extdata", "DNA-seq", "SRR054616.bw", package = "ggcoverage")
# # read CNV
# cnv.df = read.table(file = cnv.file, sep = "\t", header = TRUE)
# # load track
# track.df = LoadTrackFile(track.file = track.file, format = "bw")
# track.df$seqnames = paste0("chr", track.df$seqnames)
# # plot
# ggcoverage(data = track.df, color = "grey", region = "chr4:1-160000000",
#            mark.region = NULL, range.position = "out") +
#   geom_gc(bs.fa.seq=BSgenome.Hsapiens.UCSC.hg19) +
#   geom_cnv(cnv.df = cnv.df, bin.col = 3, cn.col = 4) +
#   geom_ideogram(genome = "hg19",plot.space = 0, highlight.centromere = TRUE)