bifurcation.diagram: plot of an haplotype bifurcation diagram

In rehh: Searching for footprints of selection using Haplotype Homozygosity based tests

Description

Haplotype Bifurcation diagram visualizes the breakdown of LD at increasing distances from the core allele at the selected focal SNPs.

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	Integer representing the number of 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

Details

Haplotype Bifurcation diagram visualizes the breakdown of LD at increasing distances from the core allele at the selected focal SNPs. The root (focal SNP) of each diagram is the core allele, identified by a vertical dashed line. The diagram is bi-directional, portraying both centromere-proximal and centromere-distal LD. Moving in one direction, each marker is an opportunity for a node; the diagram either divides or not based on whether both or only one allele is present. Thus the breakdown of LD on the core haplotype background is portrayed at progressively longer distances. The thickness of the lines corresponds to the number of samples with the indicated long- distance haplotype.

Value

The function returns a plot.

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

#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()

Example output

Loading required package: rehh.data
Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:stats':

    lowess

null device 
          1 

rehh documentation built on May 2, 2019, 5:17 p.m.