manhattanplot: Manhattan plot of iHS, XP-EHH or Rsb over a genome.

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

Description

Manhattanplot of iHS, XP-EHH or Rsb over a genome.

Usage

manhattanplot(
  data,
  pval = FALSE,
  threshold = c(-2, 2),
  chr.name = NA,
  cr = NULL,
  cr.col = "gray",
  cr.opacity = 0.5,
  cr.lab.cex = 0.6,
  cr.lab.offset = 0,
  cr.lab.pos = "top",
  mrk = NULL,
  mrk.cex = 1,
  mrk.col = "gray",
  mrk.pch = 1,
  mrk.lab.cex = 0.4,
  mrk.lab.pos = 4,
  ignore_sign = FALSE,
  cex = 0.5,
  las = 1,
  pch = 20,
  inset = 5e+06,
  resolution = NULL,
  ...
)

Arguments

data	output of either ihh2ihs, ies2xpehh or ines2rsb.
pval	logical. If TRUE, the p-value is plotted, otherwise the score itself.
threshold	a horizontal line is added at the corresponding value(s), for instance to represent a significance threshold. A single value (upper or lower threshold) or two values (upper and lower) can be specified.
chr.name	if NA (default), all chromosomes are plotted, otherwise only those specified.
cr	highlight "candidate regions" specified by a data.frame with columns CHR, START and END as obtained by the function calc_candidate_regions.
cr.col	the color for highlighting
cr.opacity	a value between 0 (invisible) and 1 (opaque).
cr.lab.cex	text size of candidate region labels.
cr.lab.offset	offset of candidate region labels.
cr.lab.pos	if "top" (default) or "bottom", candidate regions are labeled by numbers; to turn off, use "none"
mrk	highlight marker specified by a data.frame containing the colums CHR and POSITION. The row names of that data frame are taken as labels. Alternatively a vector with marker IDs can be specified. In the latter case the ID is used as label.
mrk.cex	size of marker label.
mrk.col	color of the highlighted points.
mrk.pch	type of the highlighted points.
mrk.lab.cex	text size of marker label. If zero, no labels are printed.
mrk.lab.pos	a position specifier for the text. Values of 1, 2, 3 and 4, respectively indicate positions below, to the left of, above and to the right of the highlighted marker.
ignore_sign	logical. If TRUE, absolute values are plotted.
cex	size of the points representing markers in the plot(s) (see par).
las	orientation of axis labels (see par).
pch	type of the points representing markers in the plot(s) (see points).
inset	inset (in bases) between chromosomes to avoid overlap of data points. Default: 5,000,000 bases.
resolution	Rasterize data points to the specified resolution and remove duplicate points. Defaults to NULL, i.e. no rasterization. A typical value might be c(1E5, 0.01), meaning that resolution on the x-axis (chromosomal position) is 100000 and on the y-axis (score or p-value) is 0.01.
...	further arguments to be passed to plot.default.

Details

The color of chromosomes is taken from the "Graphics Palette", see palette.

If a single chromosome is plotted, a genomic region can be specified by argument xlim.

Other statistics can be plotted as well, although a warning is issued. They must be given by a data.frame with columns CHR and POSITION and the statistic in the third column.

Value

The function returns a plot.

See Also

ihh2ihs, ies2xpehh, ines2rsb, calc_candidate_regions.

Examples

library(rehh.data)
data(wgscan.cgu)
## results from a genome scan (44,057 SNPs)
## see ?wgscan.eut and ?wgscan.cgu for details
wgscan.ihs <- ihh2ihs(wgscan.cgu)
manhattanplot(wgscan.ihs)

Example output

Discard focal markers with Minor Allele Frequency equal to or below 0.05 .
6890 markers discarded.
37167 markers remaining.

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