Panel function for plotting copy number and B allele frequencies for a genomic interval.

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Description

Panel function for plotting copy number and B allele frequencies for a genomic interval.

Usage

1
xypanelBaf(x, y, gt, baf, 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 basepairs

y

total copy number (relative or absolute)

gt

Genotypes coded as integers (1=AA, 2=AB, 3=BB). This is optional. If provided one can color code the plotting symbols by the genotype.

baf

B allele frequencies.

is.snp

Logical. Indicator of whether the marker hybridized to a known SNP or a nonpolymorphic region of the genome.

range

A RangedDataCNV-derived object indicating the genomic interval to plot.

col.hom

Color to use for homozygous genotypes.

fill.hom

Fill color to use for homozygous genotypes.

col.het

Color to use for heterozygous genotypes.

fill.het

Fill color to use for heterozygous genotypes.

col.np

Color to use for nonpolymorphic markers

fill.np

Fill color for nonpolymorphic markers.

show.state

Logical indicating whether to display the copy number state for a RangedDataHMM object.

state.cex

Size of the font for displaying the HMM state. Ignored if show.state is FALSE.

col.state

Color for displaying the state.

...

Additional arguments passed to panel.xyplot.

subscripts

See panel.xyplot

Details

Function for plotting B allele frequencing and copy number on a trellis display. Intended to be passed to the panel argument of the function xyplotLrrBaf and should not be called directly by the user.

Author(s)

R.Scharpf

See Also

xyplotLrrBaf