plotSegmentation {cancerTiming}R Documentation

plot segmentation(s) against positions

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)

[Package cancerTiming version 3.1.8 Index]