cn.mops (version 1.18.0)

segplot,CNVDetectionResult-method: Visualization of a CNV detection result.

Description

Plots the log normalized read counts and the detected segments as a segmentation plot.

Usage

"segplot"(r, mainCN = "CN2", sampleIdx, seqnames, segStat = "mean", plot.type = "s", altcol = TRUE, sbyc.layout, cbys.nchrom = 1, cbys.layout, include.means = TRUE, zeroline = TRUE, pt.pch = ".", pt.cex = 3, pt.cols = c("green", "black"), segcol = "red", zlcol = "grey", ylim, lwd = 3, ...)

Arguments

r

An instance of "CNVDetectionResult"

mainCN

The name of the main copy number. That is "CN2" for diploid individuals. For haplocn.mops this should be set to "CN1".

sampleIdx

The index of the samples to be plotted. (Default = missing)

seqnames

The names of the reference sequence (chromosomes) to be plotted. (Default = missing)

segStat

Whether the segment line should display the mean or the median of a segments calls. (Default = "mean").

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.nchrom

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

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).

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

Generates a segmentation plot.

Examples

data(cn.mops)
r <- cn.mops(X[1:200, ])
segplot(r,sampleIdx=1)