fastseg (version 1.18.0)

segPlot: Plots the data from a copy number array experiment (aCGH, ROMA etc.) along with the results of segmenting it into regions of equal copy numbers.

Description

Plots the data from a copy number array experiment (aCGH, ROMA etc.) along with the results of segmenting it into regions of equal copy numbers.

Usage

segPlot(x, res, plot.type = "chrombysample", altcol = TRUE, sbyc.layout = NULL, cbys.nchrom = 1, cbys.layout = NULL, include.means = TRUE, zeroline = TRUE, pt.pch = NULL, pt.cex = NULL, pt.cols = NULL, segcol = NULL, zlcol = NULL, ylim = NULL, lwd = NULL, ...)

Arguments

x

The object that was segmented by fastseg.

res

The result of fastseg.

plot.type

the type of plot. (Default = "s").

altcol

logical flag to indicate if chromosomes should be plotted in alternating colors in the whole genome plot. (Default = TRUE).

sbyc.layout

layout settings for the multifigure grid layout for the `samplebychrom' type. It should be specified as a vector of two integers which are the number of rows and columns. The default values are chosen based on the number of chromosomes to produce a near square graph. For normal genome it is 4x6 (24 chromosomes) plotted by rows. (Default = NULL).

cbys.layout

layout settings for the multifigure grid layout for the `chrombysample' type. As above it should be specified as number of rows and columns and the default chosen based on the number of samples. (Default = NULL).

cbys.nchrom

the number of chromosomes per page in the layout. (Default = 1).

include.means

logical flag to indicate whether segment means are to be drawn. (Default = TRUE).

zeroline

logical flag to indicate whether a horizontal line at y=0 is to be drawn. (Default = TRUE).

pt.pch

the plotting character used for plotting the log-ratio values. (Default = ".")

pt.cex

the size of plotting character used for the log-ratio values (Default = 3).

pt.cols

the color list for the points. The colors alternate between chromosomes. (Default = c("green","black").

segcol

the color of the lines indicating the segment means. (Default = "red").

zlcol

the color of the zeroline. (Default = "grey").

ylim

this argument is present to override the default limits which is the range of symmetrized log-ratios. (Default = NULL).

lwd

line weight of lines for segment mean and zeroline. (Default = 3).

...

other arguments which will be passed to plot commands.

Value

A plot of the values and segments.

Examples

data(coriell)
head(coriell)
samplenames <- colnames(coriell)[4:5]
data <- as.matrix(coriell[4:5])
chrom <- coriell$Chromosome
maploc <- coriell$Position
library("GenomicRanges")
gr <- GRanges(seqnames=chrom,
		ranges=IRanges(maploc, end=maploc))
mcols(gr) <- data
colnames(mcols(gr)) <- samplenames
res <- fastseg(gr)
segPlot(gr,res)