plotCytoband {SNPchip}R Documentation

Adds cytoband to plot.

Description

Adds cytobands to views of chromosome copy number and genotype plots.

Usage

plotCytoband(object, ...)

Arguments

object Object of class AnnotatedSnpSet
... Additional arguments to par such as xlim, cex.axis, xaxs, and main.

Details

This function is meant to primarily be called by plotSnp and displayed beneath copy number and genotype estimates.

Value

Only recommended when plotting 5 or fewer chromosomes (resolution is poor otherwise). It is possible to plot partial views of a chromosome and its cytoband as well (see examples).

Author(s)

Robert Scharpf and Jason Ting

References

See Also

plotSnp, AnnotatedSnpSet

Examples

data(annSnpset)
data(cytoband)
str(cytoband)
chr1 <- annSnpset[chromosome(annSnpset) == "1", ]

par(mfrow=c(1, 1), mar=c(0, 0, 3, 0), oma=c(5, 0, 3, 0))
plotCytoband(object=chr1, chromosome="1", main="chromosome 1")

plotSnp(chr1, 1, 5, oma=c(6, 4, 0, 3), cex=c(3,3,3),
        cex.axis=1.2, cex.legend=c(1.2, 1.2), addCytoband=TRUE,
        legend.location=c("topleft", "bottomleft"),
        height.cytoband=0.2, width.right=0.2, bty="o", cex.lab=1.5, ncol=1)

##The x-axis begins at the first SNP past the centromere
qarm <- position(chr1) > centromere(chromosomeAnnotation(annSnpset), "1")[[2]] & !is.na(position(chr1))
plotSnp(chr1[qarm, ], 1, 5, oma=c(6, 4, 0, 3), cex=rep(1,3), pch=rep(20,3),
        cex.axis=1.2, cex.legend=c(1.2, 1.2), addCytoband=TRUE,
        legend.location=c("topleft", "bottomleft"),
        height.cytoband=0.2, width.right=0.2, bty="o", cex.lab=1.5, ncol=1, xaxs="r")

##Not equivalent to previous plot because the x-axis begins at the end
##of the centromere (note that there are no SNPs close to the centromere).
qarm <- c(centromere(chromosomeAnnotation(annSnpset), "1")[[2]],
          chromosomeSize(chromosomeAnnotation(annSnpset), "1")[[1]])
plotSnp(chr1, 1, 5, oma=c(6, 4, 0, 3), cex=c(1, 1, 1), pch=rep(20, 3),
        cex.axis=1.2, cex.legend=c(1.2, 1.2), addCytoband=TRUE,
        legend.location=c("topleft", "bottomleft"),
        height.cytoband=0.2, width.right=0.2, bty="o", cex.lab=1.5, ncol=1, adj=0,
        xlim=qarm)

[Package SNPchip version 1.0.0 Index]