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Last data update: 2014.03.03

R: Plot copy number heatmap

plotHeatmap

R Documentation

Plot copy number heatmap

Description

Heatmap reflecting the magnitude of estimated copy numbers relative to some pre-defined limits. Estimates may be obtained using pcf or multipcf, and results may be visualized over the entire genome or by chromosomes.

Usage

plotHeatmap(segments, upper.lim, lower.lim = -upper.lim, pos.unit = "bp", 
    chrom = NULL, layout = c(1, 1),...)

Arguments

`segments`	a data frame containing the segmentation results found by either `pcf` or `multipcf`.
`upper.lim`	a positive numeric vector giving the upper limits(s) to be applied. The colors in the heatmap will reflect the magnitude of the estimated copy numbers relative to this limit, see details.
`lower.lim`	a negative numeric vector of same length as `upper.lim` giving the lower limits(s) to be applied. Default is to use the negative value of `upper.lim`.
`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 three giving the colors to interpolate in the heatmap, default is c("dodgerblue","black","red"). `n.col` an integer giving the number of color shades to be applied in the interpolation, default is 50. `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. Default is 0, which implies that there is no space. `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 segments are represented by a rectangle plotted in a color corresponding to the difference between the segment copy number value and the limits. If the value is below lower.lim, the color of the rectangle will equal the input in colors[1] (default dodgerblue). If the value is above lower.lim, but below zero, the color of the rectangle will be a nuance between the input in colors[1] and colors[2] (default black). The closer the value is to zero, the closer the nuance will be to colors[2]. Similary, if the value is above upper.lim, the color of the rectangle will equal the input in colors[3] (default red), whereas if the value is below upper.lim, but above zero, the color will be a nuance between the input in colors[2] and colors[3]. Again, the closer the value is to zero, the closer the nuance will be to colors[2].

Each row in the heatmap 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)

#Heatmap for entire genome, two limit values:
plotHeatmap(segments=seg,upper.lim=c(0.1,0.5),layout=c(2,1))

#Heatmap for the first 4 chromosomes:
plotHeatmap(segments=seg,upper.lim=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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/plotHeatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotHeatmap
> ### Title: Plot copy number heatmap
> ### Aliases: plotHeatmap
> 
> ### ** 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 
> 
> #Heatmap for entire genome, two limit values:
> plotHeatmap(segments=seg,upper.lim=c(0.1,0.5),layout=c(2,1))
> 
> #Heatmap for the first 4 chromosomes:
> plotHeatmap(segments=seg,upper.lim=0.1,chrom=c(1:4),layout=c(2,2))
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>