plotCopies {cancerTiming}

plot segmentation values against each other

Description

Plot different values per segment against each other (e.g. minor and major allele estimates).

Usage

plotCopies	(x, y, nX, nY, xleg, yleg, onlyPositive = TRUE,
	                 equalAxis = TRUE, integerLegend = TRUE, xlim, ylim, ...)

Arguments

x

The values plotted for x coordinates (e.g. segmentation value for minor allele)

y

The values plotted for y coordinates (e.g. segmentation value for major allele)

nX

The grouping id for the x coordinate (e.g. assignment of number of copies)

nY

The grouping id for the y coordinate (e.g. assignment of number of copies)

xleg

title for the legend of the x values

yleg

title for the legend of the y values

xlim

limits for the x axis

ylim

limits for the y axis

onlyPositive

only plot values positive in x and y

equalAxis

xlim and ylim are forced to be the same

integerLegend

Only give integers

...

passed to the scatter plot command

Author(s)

Elizabeth Purdom

Examples

cp1<-c(0,0,0,1,1,1,1,2,2,2,3,3,3)
cp2<-c(0,1,2,1,2,2,3,2,2,4,3,6,8)
seg1<-jitter(c(0,0,0,1,1,1,1,2,2,2,3,3,3))
seg2<-jitter(c(0,1,2,1,2,2,3,2,2,4,3,6,8))
plotCopies(x=seg1,y=seg2,nX=cp1,nY=cp2)