Description Usage Arguments Author(s) Examples
Graphically displays regions of any ibd sharing, no ibd sharing and no calls along a chromosome for a set of haplotypes / pair of genotypes.
1 2 |
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 |
MD Brown
1 2 3 4 5 6 7 8 9 10 11 12 13 14 | ## 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="")
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