rehh (version 2.0.4)

bifurcation.diagram: plot of an haplotype bifurcation diagram

Description

A haplotype bifurcation diagram visualizes the decay of EHH of a "core" allele of a focal SNP at increasing distances.

Usage

bifurcation.diagram(haplohh, mrk_foc, all_foc=1, nmrk_l=10, nmrk_r=10,
                limhapcount = 10, refsize = 0.1, linecol = "blue",
                main_leg = NA, xlab_leg = "Position")

Arguments

haplohh

An object of class haplohh (see data2haplohh).

mrk_foc

Either the number of the marker in the haplohh object (as integer) or its name (as string) to specify the focal marker

all_foc

either 1 or 2 depending on the chosen core allele (resp. ancestral or derived)

nmrk_l

Number of markers to be considered upstream of the focal SNP

nmrk_r

Number of markers to be considered downstream of the focal SNP

limhapcount

Minimal number of haplotypes containing the core allele at the focal SNP

refsize

Controls the relative width of the diagram lines on the plot

linecol

Color of the lines on the diagram

main_leg

Main legend of the diagram. By default, the name of the SNP together with the allele considered

xlab_leg

Legend on the xaxis of the diagram

Value

The function returns a plot.

Details

The function `bifurcation.diagram()` draws haplotype bifurcation diagrams [@Sabeti2002] that visualize the decay of EHH around a focal SNP. A stark contrast of ancestral and derived bifurcation diagrams should correspond to outlier values of ihs. In the plot the root (focal SNP) is identified by a vertical dashed line. The diagram is bi-directional, portraying decay along both sides of the focal SNP. Moving in one direction, each marker is an opportunity for a bifurcation further differentiating (extended) haplotypes. The thickness of the lines corresponds to the number of chromosomes with the same extended haplotype.

References

Sabeti, P.C. and Reich, D.E. and Higgins, J.M. and Levine, H.Z.P and Richter, D.J. and Schaffner, S.F. and Gabriel, S.B. and Platko, J.V. and Patterson, N.J. and McDonald, G.J. and Ackerman, H.C. and Campbell, S.J. and Altshuler, D. and Cooper, R. and Kwiatkowski, D. and Ward, R. and Lander, E.S. (2002). Detecting recent positive selection in the human genome from haplotype structure. Nature, 419, 832--837.

Examples

# NOT RUN {
#example haplohh object (280 haplotypes, 1424 SNPs)
#see ?haplohh_cgu_bta12 for details
data(haplohh_cgu_bta12)
#plotting bifurcation diagram for both ancestral and derived allele
#from the focal SNP at position 456
#which display a strong signal of selection
layout(matrix(1:2,2,1))
#ancestral allele
bifurcation.diagram(haplohh_cgu_bta12,mrk_foc=456,all_foc=1,
nmrk_l=20,nmrk_r=20)
#derived allele
bifurcation.diagram(haplohh_cgu_bta12,mrk_foc=456,all_foc=2,
nmrk_l=20,nmrk_r=20)
##
dev.off()
# }