plot.ehhs {rehh}

Plot EHHS around a focal marker

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)