ibdhap.barplot: create ibd barplot

In IBDhaploRtools: Functions for the Analysis of IBD Haplo Output.

Description

Graphically displays regions of any ibd sharing, no ibd sharing and no calls along a chromosome for a set of haplotypes / pair of genotypes.

Usage

ibdhap.barplot(x, data.type = c("h", "g", "r"), col = c("grey", "red",
"white"), position = NA, top = 1, bottom = 0, density = 50, ...)

Arguments

x	A vector of ibd states (with values 0 - 15 for haplotypic, 0-9 genotypic, one for each marker). This is expected to be a single column taken from the output of ibdhap.make.states.
data.type	"h" : haplotypic data "g" : genotypic data (or hap data ran as genotypic) "r" : reduced data (output from running ibdhap.reduce.states and then ibdhap.make.states)
col	Vector consisting of three colors. The colors represent no calls, any ibd shared, and no ibd shared, respectively.
position	A position vector, with the same length as x describing the positions (in cM, M, or any other metric) of each marker. If positions is not included, "segment length" refers to number of SNPs making up a segment.
top	top value of rectangles in barplot
bottom	bottom value of rectangles in barplot
density	density of diagonal lines filling each segment in lines per sq inch.
...	additional graphical parameters

Author(s)

MD Brown

Examples

## this example is taken from the package vignette.
##See vignette(IBDhaploRtools_tutorial)

data(qibd_phased)
data(ids_phased)

phased.gold <- ibdhap.make.calls( qibd.file  = qibd_phased,
                   ids.file= ids_phased, cutoff = 0.8)

par(mfrow=c(4,1)) 
ibdhap.barplot(phased.gold[,1], data.type="h", xlab="", ylab="") 
ibdhap.barplot(phased.gold[,2], data.type="h", xlab="", ylab="")
ibdhap.barplot(phased.gold[,3], data.type="h", xlab="", ylab="")
ibdhap.barplot(phased.gold[,4], data.type="h", xlab="", ylab="")

IBDhaploRtools documentation built on May 2, 2019, 6:48 p.m.