plotCopies: plot segmentation values against each other

In cancerTiming: Estimation of Temporal Ordering of Cancer Abnormalities

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)

Example output

cancerTiming documentation built on May 2, 2019, 9:28 a.m.