plot.furcation: Plots furcation trees around a focal marker

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

Description

Plots furcation trees around a focal marker

Usage

## S3 method for class 'furcation'
plot(
  x,
  allele = NA,
  col = c("blue", "red", "violet", "orange"),
  mrk.col = "gray",
  lwd = 0.1,
  hap.names = NULL,
  cex.lab = 1,
  family.lab = "",
  offset.lab = 0.5,
  legend = NA,
  legend.xy.coords = "automatic",
  ...
)

Arguments

x	an object of class furcation (see calc_furcation).
allele	If NA (default), furcation trees for all alleles of the focal marker are plotted, otherwise for the specified alleles. Alleles must be specified by their internal coding, i.e. '0' for ancestral resp. major allele, etc.
col	color for each allele (as coded internally).
mrk.col	color of the vertical line at the focal marker position.
lwd	controls the relative width of the diagram lines on the plot (default 0.1).
hap.names	a vector containing names of chromosomes.
cex.lab	relative size of labels. See par.
family.lab	font family for labels. See par.
offset.lab	offset of labels. 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 argument is passed to legend.
...	other arguments to be passed to plot.default.

See Also

plot.haplen.

Examples

#example haplohh object (280 haplotypes, 1424 SNPs)
#see ?haplohh_cgu_bta12 for details
data(haplohh_cgu_bta12)
#plotting furcation diagram for both ancestral and derived allele
#from the marker "F1205400"
#which display a strong signal of selection
f <- calc_furcation(haplohh_cgu_bta12, mrk = "F1205400")
plot(f)
plot(f, xlim = c(2e+07,3.5e+07))
plot(f, xlim = c(2.7e+07,3.1e+07))
plot(f, xlim = c(2.7e+07,3.1e+07), hap.names = hap.names(haplohh_cgu_bta12), cex.lab=0.3)

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