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Last data update: 2014.03.03

R: Plot areas with copy number aberrations

plotAberration

R Documentation

Plot areas with copy number aberrations

Description

Create plots reflecting the location of aberrated segments. Results may be visualized over the entire genome or by chromosomes.

Usage

plotAberration(segments, thres.gain, thres.loss = -thres.gain, pos.unit = "bp", 
    chrom = NULL, layout = c(1, 1),...)

Arguments

`segments`	a data frame containing the segmentation results found by either `pcf` or `multipcf`.
`thres.gain`	a numeric vector giving the threshold value(s) to be applied for calling gains.
`thres.loss`	a numeric vector of same length as `thres.gain` giving the threshold value(s) to be applied for calling losses. Default is to use the negative value of `thres.gain`.
`pos.unit`	the unit used to represent the probe positions. Allowed options are "mbp" (mega base pairs), "kbp" (kilo base pairs) or "bp" (base pairs). By default assumed to be "bp".
`chrom`	a numeric or character vector with chromosome number(s) to indicate which chromosome(s) is (are) to be plotted. If unspecified the whole genome is plotted.
`layout`	the vector of length two giving the number of rows and columns in the plot window. Default is `c(1,1)`.
`...`	other optional graphical parameters. These include the plot arguments `xlab`, `ylab`, `main`, `cex.main`, `mgp`, `cex.lab`, `cex.axis`, `mar` and `title` (see `par` on these), as well as `plot.size`, `plot.unit`, `plot.ideo`, `ideo.frac`, `cyto.text`, `assembly` and `cex.cytotext` (see `plotSample` on these). In addition, a range of graphical arguments specific for this plot function may be specified: `colors` a character vector of length two where the first and second element specifies the color used to represent loss and gain, respectively. Default is c("dodgerblue","red"). `sample.labels` a logical value indicating whether sample labels are to be plotted along the y-axis. Default is TRUE. `sep.samples` a number in the range 0 to 0.4 used to create some space between samples. 0 implies that there is no space. Default is 2/nsample, where nsample is the number of samples found in `segments`. `sample.line` a numeric scalar giving the margin line where the sample labels should be written, starting at 0 counting outwards. Default is 0.2. `sample.cex` the size of the sample labels.

Details

For each sample, the aberrated regions are shown in the color specified in colors[1] (default dodgerblue) if the segment value is below thres.loss and the color specified in colors[2] (default red) if the segment value is above thres.gain. Non-aberrated regions are shown in white. Each row in the plot represents a sample, while probe positions are reflected along the x-axis.

Note

This function applies par(fig), and is therefore not compatible with other setups for arranging multiple plots in one device such as par(mfrow,mfcol).

Author(s)

Gro Nilsen

Examples

#Load lymphoma data
data(lymphoma)

#Run pcf to obtain estimated copy number values
seg <- pcf(data=lymphoma,gamma=12)

#Plot aberrations for the entire genome
plotAberration(segments=seg,thres.gain=0.15)

#Plot aberrations for the first 4 chromosomes:
plotAberration(segments=seg,thres.gain=0.1,chrom=c(1:4),layout=c(2,2))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(copynumber)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/copynumber/plotAberration.rd_%03d_medium.png", width=480, height=480)
> ### Name: plotAberration
> ### Title: Plot areas with copy number aberrations
> ### Aliases: plotAberration
> 
> ### ** Examples
> 
> #Load lymphoma data
> data(lymphoma)
> 
> #Run pcf to obtain estimated copy number values
> seg <- pcf(data=lymphoma,gamma=12)
pcf finished for chromosome arm 1p 
pcf finished for chromosome arm 1q 
pcf finished for chromosome arm 2p 
pcf finished for chromosome arm 2q 
pcf finished for chromosome arm 3p 
pcf finished for chromosome arm 3q 
pcf finished for chromosome arm 4p 
pcf finished for chromosome arm 4q 
pcf finished for chromosome arm 5p 
pcf finished for chromosome arm 5q 
pcf finished for chromosome arm 6p 
pcf finished for chromosome arm 6q 
pcf finished for chromosome arm 7p 
pcf finished for chromosome arm 7q 
pcf finished for chromosome arm 8p 
pcf finished for chromosome arm 8q 
pcf finished for chromosome arm 9p 
pcf finished for chromosome arm 9q 
pcf finished for chromosome arm 10p 
pcf finished for chromosome arm 10q 
pcf finished for chromosome arm 11p 
pcf finished for chromosome arm 11q 
pcf finished for chromosome arm 12p 
pcf finished for chromosome arm 12q 
pcf finished for chromosome arm 13q 
pcf finished for chromosome arm 14q 
pcf finished for chromosome arm 15q 
pcf finished for chromosome arm 16p 
pcf finished for chromosome arm 16q 
pcf finished for chromosome arm 17p 
pcf finished for chromosome arm 17q 
pcf finished for chromosome arm 18p 
pcf finished for chromosome arm 18q 
pcf finished for chromosome arm 19p 
pcf finished for chromosome arm 19q 
pcf finished for chromosome arm 20p 
pcf finished for chromosome arm 20q 
pcf finished for chromosome arm 21q 
pcf finished for chromosome arm 22q 
pcf finished for chromosome arm 23p 
pcf finished for chromosome arm 23q 
> 
> #Plot aberrations for the entire genome
> plotAberration(segments=seg,thres.gain=0.15)
> 
> #Plot aberrations for the first 4 chromosomes:
> plotAberration(segments=seg,thres.gain=0.1,chrom=c(1:4),layout=c(2,2))
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>