plotFocals: plotFocals

In bernatgel/FindFocals: Find focal gains & deletions in SNP array data

Description

Plots the SNP array data with the identified focal gains and losses on top.

Usage

plotFocals(find.focal.results,
plot.gain=TRUE, plot.gain.points=FALSE, gain.col="#FFBD07AA", gain.border.col="#FFBD07AA",
plot.del=TRUE, plot.del.points=FALSE, del.col="#00A6EDAA", del.border.col="#00A6EDAA",
plot.mean.lrr=FALSE, mean.lrr.col="#B0FFA5AA", mean.lrr.border.col=NA, mean.lrr.line.col="#FF7C30",
main="Focal Gains and Losses", chromosomes="canonical", zoom=NULL,
lrr.min=-4, lrr.max=2, total.height=1, bottom=0, margin=0.05,
focal.points.cex=0.6, points.cex=0.3, labels.cex=1.5, main.cex=2, axis.cex=1.2, chr.cex=1.5)

Arguments

find.focal.results	The results from findFocals
plot.gain	(defaults to TRUE)
plot.gain.points	(defaults to FALSE)
gain.col	(defaults to "#FFBD07AA")
gain.border.col	(defaults to "#FFBD07AA")
plot.del	(defaults to TRUE)
plot.del.points	(defaults to FALSE)
del.col	(defaults to "#00A6EDAA")
del.border.col	(defaults to "#00A6EDAA")
plot.mean.lrr	(defaults to FALSE)
mean.lrr.col	(defaults to "#B0FFA5AA")
mean.lrr.border.col	(defaults to NA)
mean.lrr.line.col	(defaults to "#FF7C30")
main	(defaults to "Focal Gains and Losses")
chromosomes	(defaults to "canonical")
zoom	(defaults to NULL)
lrr.min	(defaults to -4)
lrr.max	(defaults to 2)
total.height	(defaults to 1)
bottom	(defaults to 0)
margin	(defaults to 0.05)
focal.points.cex	(defaults to 0.6)
points.cex	(defaults to 0.3)
labels.cex	(defaults to 1.5)
main.cex	(defaults to 2)
axis.cex	(defaults to 1.2)
chr.cex	(defaults to 1.5)

Details

Creates a plot with the LRR and BAF values along the genome and adds rectangles showing the identified focal gains and deletions. Optionally, the SNPs in each of the focal events may be highlighted.

Value

Invisibly returns the karyoplot object representing the plot. With it it is possible to add other elements to the plot using standrad karyoploteR functions

bernatgel/FindFocals documentation built on May 3, 2019, 9:04 p.m.