plotSegmentation: plot segmentation(s) against positions

In epurdom/cancerTiming: Estimation of Temporal Ordering of Cancer Abnormalities

Description

Plot the values of a segmentation against chromosome position.

Usage

plotSegmentation(segs, valId, col = palette(),lty=1, lwd = 2, xlim, ylim,
	xlab="Position", ylab = valId,...)

Arguments

segs	list of segmentation data.frames. Each data.frame must have ‘start’ and ‘end’ as the column names of the limits of the segmentations.
valId	name of the column with the segmentation value to be plotted (must be the same in all data.frames)
col	colors for the segmentation (1 per element of the list of segmentations)
lty	lty for the lines
lwd	lwd for the lines
xlim	x limits
ylim	y limits
xlab	The label for the x-axis
ylab	The label for the y-axis
...	passed to initial plotting command

Value

returns invisibly the col and lty after any processing done, useful for legends.

Author(s)

Elizabeth Purdom

Examples

data(mutData)
segData<-data.frame(chromosome="17",start=c(0,1.8e7+1),
	end=c(1.8e7,max(mutData$position)),val=c(2,3))
cp1<-data.frame(chromosome="17",start=c(0,1.8e7+1),
	end=c(1.8e7,max(mutData$position)),val=c(1,1))
cp2<-data.frame(chromosome="17",start=c(0,1.8e7+1),
	end=c(1.8e7,max(mutData$position)),val=c(.9,2))
out<-plotSegmentation(list(total=segData,cp1=cp1,cp2=cp2),
	valId="val",lwd=2,ylab="Segmentation Value")
legend("topright",names(out),fill=out)

epurdom/cancerTiming documentation built on May 16, 2019, 8:21 a.m.