segplot,CNVDetectionResult-method {cn.mops} | R Documentation

## Visualization of a CNV detection result.

### Description

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

### Usage

    ## S4 method for signature 'CNVDetectionResult'
    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.

### Author(s)

Guenter Klambauer klambauer@bioinf.jku.at

### Examples

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

[Package cn.mops version 1.26.0 Index]