plot.haplohh: Plot the variants of a haplohh object

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

Description

Plot the variants of a haplohh object. This method is intended for visualization of very small data sets such as the examples provided by the package.

Usage

## S3 method for class 'haplohh'
plot(
  x,
  mrk = NA,
  allele = NA,
  group_by_allele = FALSE,
  ignore.distances = FALSE,
  col = c("blue", "red", "violet", "orange"),
  linecol = "gray",
  mrk.col = "gray",
  pch = 19,
  cex = 1,
  lwd = 1,
  hap.names = NULL,
  mrk.names = NULL,
  cex.lab.hap = 0.8,
  cex.lab.mrk = 0.8,
  family.lab = "",
  offset.lab.hap = 0.5,
  offset.lab.mrk = 0.25,
  pos.lab.hap = "left",
  pos.lab.mrk = "top",
  srt.hap = 0,
  srt.mrk = 0,
  highlight.mrk = NULL,
  highlight.mrk.col = c("lightgray", "black", "darkgray"),
  ...
)

Arguments

x	an object of class haplo-hh generated by data2haplohh.
mrk	the focal marker. Used only, if alleles are grouped or (de-)selected.
allele	if NA (default), haplotypes of all alleles are plotted, otherwise for the specified alleles. Alleles must be specified by their internal coding, i.e. '0' for ancestral resp. major allele, etc. Haplotypes with missing values at the focal marker can only be selected in combination with genotyped alleles, e.g. as c(1,NA).
group_by_allele	logical. If TRUE, group chromosomes by their allele at the focal marker; alleles are ordered by their internal coding unless parameter alleles is specified. If FALSE (default), haplotypes are drawn by their order in the input file.
ignore.distances	logical. If TRUE, markers are drawn equally-spaced.
col	color for each allele (as coded internally).
linecol	the color of the background lines. If more than one color is specified and sequences sorted by the marker allele, the specified colors are used to distinguish the alleles; otherwise consecutive sequences are set into the specified colors.
mrk.col	color of the vertical line at the focal marker position.
pch	symbol used for markers. See points.
cex	relative size of marker symbol. See points.
lwd	line width.
hap.names	a vector containing the names of chromosomes.
mrk.names	a vector containing the names of markers.
cex.lab.hap	relative letter size of haplotype labels. See par.
cex.lab.mrk	relative letter size of marker labels. See par.
family.lab	font family for labels. See par.
offset.lab.hap	offset of haplotype labels. See par.
offset.lab.mrk	offset of marker labels. See par.
pos.lab.hap	position of haplotype labels. Either "left" (default), "right", "none" or "both".
pos.lab.mrk	position of marker labels. Either "top" (default) or "none".
srt.hap	rotation of haplotype labels (see par).
srt.mrk	rotation of marker labels (see par).
highlight.mrk	vector of markers to be highlighted
highlight.mrk.col	color for each allele (as coded internally) at highlighted markers.
...	other parameters to be passed to plot.default.

Details

Specifying a haplohh-object with more than 4096 haplotypes or markers produces an error.

See Also

calc_haplen, plot.furcation.

Examples

#example haplohh object
make.example.files()
hh <- data2haplohh(hap_file = "example1.hap",
                   map_file = "example1.map",
                   allele_coding = "01")
plot(hh)
hh <- data2haplohh(hap_file = "example2.hap",
                   map_file = "example2.map",
                   allele_coding = "01",
                   min_perc_geno.mrk = 50)
plot(hh)
remove.example.files()

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