plot.ehhs: Plot EHHS around a focal marker

In rehh: Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests

Description

Plot curve of EHHS values around a focal marker.

Usage

## S3 method for class 'ehhs'
plot(
  x,
  nehhs = FALSE,
  ylim = c(0, 1),
  type = "l",
  main = paste0("EHHS around '", x$mrk.name, "'"),
  xlab = "Position",
  ylab = "Extended Haplotype Homozygosity per Site",
  bty = "n",
  mrk.col = "gray",
  ...
)

Arguments

x	data (output of calc_ehhs).
nehhs	logical. If TRUE, plot normalized EHHS.
ylim	the y limits of the plot
type	plot type (see codeplot.default. Type "s" or "S" yield both (the same) piecewise constant curve.
main	title for the plot (default NA, i.e. none).
xlab	title for the x-axis.
ylab	title for the y-axis.
bty	box type around plot (see par).
mrk.col	color of the vertical line at the focal marker position.
...	further arguments to be passed to function plot.default.

See Also

data2haplohh, plot.ehh, calc_ehhs, scan_hh.

Examples

#example haplohh object (280 haplotypes, 1424 SNPs)
#see ?haplohh_cgu_bta12 for details
data(haplohh_cgu_bta12)
#computing EHHS statisitics for the marker "F1205400"
#which displays a strong signal of selection
ehhs <- calc_ehhs(haplohh_cgu_bta12, mrk = "F1205400")
plot(ehhs)

rehh documentation built on Sept. 15, 2021, 5:06 p.m.