IBDhaploRtools (version 1.8)

ibdhap.barplot: create ibd barplot

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

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="")