plot.ehh: Plot EHH around a focal marker

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

Description

Plot curve of EHH values around a focal marker.

Usage

## S3 method for class 'ehh'
plot(
  x,
  ylim = c(0, 1),
  type = "l",
  main = paste0("EHH around '", x$mrk.name, "'"),
  xlab = "Position",
  ylab = "Extended Haplotype Homozygosity",
  col = c("blue", "red", "violet", "orange"),
  mrk.col = "gray",
  bty = "n",
  legend = NA,
  legend.xy.coords = "automatic",
  ...
)

Arguments

x	data (output of calc_ehh).
ylim	the y limits of the plot
type	plot type (see codeplot.default and matplot). 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.
col	color for the ancestral and derived alleles (respectively) curves.
mrk.col	color of the vertical line at the focal marker position.
bty	box type around plot (see par).
legend	legend text.
legend.xy.coords	if "automatic" (default) places legend either top left or top right; if "none", no legend is drawn; otherwise the argument is passed to legend.
...	further arguments to be passed to function matplot.

See Also

data2haplohh, calc_ehh, plot.ehhs, scan_hh.

Examples

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

Example output

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