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Last data update: 2014.03.03

R: A panel function for plotting copy number versus physical...

xypanel

R Documentation

A panel function for plotting copy number versus physical position

Description

A panel function for xyplot for plotting copy number versus physical position.

Usage

xypanel(x, y, gt, is.snp, range, col.hom = "grey20", fill.hom =
"lightblue", col.het = "grey20", fill.het = "salmon", col.np = "grey20",
fill.np = "grey60", show.state=TRUE, state.cex=1,  col.state="blue", ..., subscripts)

Arguments

`x`	Physical position in megabases.
`y`	Copy number estimates.
`gt`	Genotype calls.
`is.snp`	Logical. Whether the marker is polymorphic.
`range`	A `RangedData` or `IRanges` object. Note that we expect the units returned by `start` and `end` to be basepairs.
`col.hom`	A specification for the color of plotting symbols for homozygous genotypes.
`fill.hom`	A specification for the fill color of plotting symbols for homozygous genotypes.
`col.het`	A specification for the color of plotting symbols for heterozygous genotypes.
`fill.het`	A specification for the fill color of plotting symbols for heterozygous genotypes.
`col.np`	A specification for the color of plotting symbols for nonpolymorphic markers.
`fill.np`	A specification for the fill color of plotting symbols for nonpolymorphic genotypes.
`show.state`	Logical. Whether to display the predicted state in each panel.
`state.cex`	Numeric. `cex` for state label. Ignored if `show.state` is `FALSE`.
`col.state`	Character. color for state label. Ignored if `show.state` is `FALSE`.
`...`	Additional arguments passed to lattice functions `xyplot`, `lpoints`, and `lrect`.
`subscripts`	See the panel functions in lattice for more information.

Details

The order of plotting is (1) nonpolymorphic markers, (2), homozygous SNPs, and (3) heterozygous SNPs. Stretches of homozygosity should appear as blue using the default color scheme.

Note

To make the drawing of the range object border invisible, one can use border="white".

Author(s)

R. Scharpf

Examples

## Not run: 
	if(require("crlmm") && require("VanillaICE") && require("IRanges")){
		library(oligoClasses)
		data(cnSetExample, package="crlmm")
		cnSetExample <- chromosomePositionOrder(cnSetExample)
		oligoSet <- as(cnSetExample, "oligoSnpSet")
		fit2 <- hmm(oligoSet, p.hom=1)
		xyplot(cn ~ x | range, data=oligoSet, range=fit2[1:10, ],
		       frame=2e6,
		       panel=xypanel, cex=0.3, pch=21, border="blue",
		       scales=list(x="free"),
		       col.hom="lightblue", col.het="salmon", col.np="grey60",
		       fill.np="grey60",
		       xlab="Mb")
		## if xyplot method is masked by lattice, do
		##xyplot <- VanillaICE:::xyplot
	}

## End(Not run)