Last data update: 2014.03.03

 R: Plot copy number data and/or segmentation results by sample
plotSampleR Documentation

Plot copy number data and/or segmentation results by sample

Description

Plot copy number data and/or segmentation results for each sample separately with chromosomes in different panels.

Usage

plotSample(data = NULL, segments = NULL, pos.unit = "bp", sample = NULL,
            chrom = NULL, assembly = "hg19", winsoutliers = NULL, xaxis = 
            "pos", layout = c(1,1), plot.ideo = TRUE, ...)

Arguments

data

a data frame with numeric or character chromosome numbers in the first column, numeric local probe positions in the second, and numeric copy number data for one or more samples in subsequent columns. The header of the copy number columns should be the sample IDs.

segments

a data frame or a list of data frames containing the segmentation results found by either pcf or multipcf.

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".

sample

a numeric vector indicating which sample(s) is (are) to be plotted. The number(s) should correspond to the sample's place (in order of appearance) in data, or in segments in case data is unspecified.

chrom

a numeric or character vector with chromosome number(s) to indicate which chromosome(s) is (are) to be plotted.

assembly

a string specifying which genome assembly version should be applied to define the chromosome ideogram. Allowed options are "hg19", "hg18", "hg17" and "hg16" (corresponding to the four latest human genome annotations in the UCSC genome browser).

winsoutliers

an optional data frame of the same size as data identifying observations classified as outliers by winsorize. If specified, outliers will be marked by a different color and symbol than the other observations (see wins.col and wins.pch).

xaxis

either "pos" or "index". The former implies that the xaxis will represent the genomic positions, whereas the latter implies that the xaxis will represent the probe index. Default is "pos".

layout

an integer vector of length two giving the number of rows and columns in the plot. Default is c(1,1).

plot.ideo

a logical value indicating whether the chromosome ideogram should be plotted. Only applicable when xaxis="pos".

...

other graphical parameters. These include the common plot arguments xlab, ylab, main, xlim, ylim, col (default is "grey"), pch (default is 46, equivalent to "."), cex, cex.lab, cex.main, cex.axis, las, tcl, mar and mgp (see par on these). In addition, a range of graphical arguments specific for plotSample (as well as the similar functions plotChrom, plotGenome and plotAllele) may be specified:

dir.print:

an optional directory where the plot(s) is (are) to be saved as pdf file(s). Defaults to NULL which implies that the plot(s) is (are) printed to screen instead.

file.name

an optional character vector containing file name(s) for the pdf file(s) to be saved.

onefile:

logical value indicating whether all plots should be plotted in one device / saved in one file. Default is TRUE. If FALSE, a new window is opened or a new file is saved for each sample (each chromosome for plotChrom).

plot.size:

a numeric vector of length 2 giving the width and height of the plotting window. Default is c(11.6,8.2).

title:

an overall title for all plots on one page.

plot.unit:

the desired unit to be applied for probe position tick marks along the x-axis. Only "mbp" (default) and "kbp" is allowed.

equalRange:

logical value indicating whether the range of the y-axis should be the same across all plots. Defaults to TRUE.

q:

a numerical value in the range 0 to 1 indicating that ylim will be set to only include observations between the (1-q/2)- and the (q/2)-quantile. Observations that fall outside these quantiles are truncated to the limits of the plot, and are by default marked by a special symbol (see q.pch). Default is q=0.01 when data is specified, and q=0 otherwise.

q.col, wins.col:

colors used to plot truncated observations and outliers. Default is "grey" and "magenta", respectively.

q.pch, wins.pch:

symbols used to plot truncated observations and outliers. Default is 42 (equivalent to "*") for both. Note that input must be of the same class as pch (numeric or character).

q.cex, wins.cex:

magnification used for truncated observations and outliers relative to cex. Default is 0.4 for both.

h:

a numerical value indicating that a horizontal reference line should be plotted at y=h. Default is h=0. h=NULL suppresses the plotting of a reference line.

at.x:

the points at which tick-marks on x-axis are to be drawn.

at.y:

the points at which tick-marks on y-axis are to be drawn.

main.line:

the margin line for the main title.

legend:

either a logical value indicating whether legends should be added to the plot if there is more than one segmentation result present in segments, or a character vector giving the legend texts to be used for the segmentation results. Default is TRUE, in which case the legend will be plotted in the topright corner of each plot.

seg.col:

color(s) used to plot the segmentation result(s). The default colors are found using the function rainbow(n), where n is the number of segmentation results found in segments (see rainbow for details).

seg.lty:

the line type(s) used to plot the segmentation result(s). Default is 1.

seg.lwd:

the line width(s) used to plot the segmentation result(s).

connect:

logical value indicating whether segments should be connected by vertical lines, default is TRUE.

ideo.frac:

a numerical value in the range 0 to 1 indicating the fraction of the plot to be occupied by the chromosome ideogram.

cyto.text:

a logical value indicating whether cytoband-names should be plotted along with the ideogram. Not recommended when many plots are plotted in the same grid, default is FALSE.

cex.cytotext:

the magnification used for the plotting of the cytoband-names.

cex.chrom:

the text size used to plot chromosome numbers in plotGenome.

Details

Several plots may be produced on the same page with the layout option. If the number of plots exceeds the desired page layout, the user is prompted before advancing to the next page of output.

Note

These functions apply par(fig), and are therefore not compatible with other setups for arranging multiple plots in one device such as par(mfrow,mfcol).

Author(s)

Gro Nilsen

See Also

plotChrom, plotGenome

Examples

#Lymphoma data
data(lymphoma)
#Take out a smaller subset of 6 samples (using subsetData):
sub.lymphoma <- subsetData(lymphoma,sample=1:6)

#Winsorize data:
wins.data <- winsorize(data=sub.lymphoma)

#Use pcf to find segments:        
uni.segments <- pcf(data=wins.data,gamma=12)

#Use multipcf to find segments as well:
multi.segments <- multipcf(data=wins.data,gamma=12)

#Plot data and pcf-segments for one sample separately for each chromosome:
plotSample(data=sub.lymphoma,segments=uni.segments,sample=1,layout=c(5,5))
#Add cytoband text to ideogram (one page per chromosome to ensure sufficient 
#space)
plotSample(data=sub.lymphoma,segments=uni.segments,sample=1,layout=c(1,1),
    cyto.text=TRUE)
#Add multipcf-segmentation results, drop legend
plotSample(data=sub.lymphoma,segments=list(uni.segments,multi.segments),sample=1,
    layout=c(5,5),seg.col=c("red","blue"),seg.lwd=c(3,2),legend=FALSE)
#Plot by chromosome for two samples, but only chromosome 1-9. One window per 
#sample:
plotSample(data=sub.lymphoma,segments=list(uni.segments,multi.segments),sample=
    c(2,3),chrom=c(1:9),layout=c(3,3),seg.col=c("red","blue"),
    seg.lwd=c(3,2),onefile=FALSE)

#Zoom in on a particular region by setting xlim:    
plotSample(data=sub.lymphoma,segments=uni.segments,sample=1,chrom=1,plot.ideo=
    FALSE,xlim=c(140,170))

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.

R is a collaborative project with many contributors.
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/plotSample.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotSample
> ### Title: Plot copy number data and/or segmentation results by sample
> ### Aliases: plotSample
> 
> ### ** Examples
> 
> #Lymphoma data
> data(lymphoma)
> #Take out a smaller subset of 6 samples (using subsetData):
> sub.lymphoma <- subsetData(lymphoma,sample=1:6)
> 
> #Winsorize data:
> wins.data <- winsorize(data=sub.lymphoma)
winsorize finished for chromosome arm 1p 
winsorize finished for chromosome arm 1q 
winsorize finished for chromosome arm 2p 
winsorize finished for chromosome arm 2q 
winsorize finished for chromosome arm 3p 
winsorize finished for chromosome arm 3q 
winsorize finished for chromosome arm 4p 
winsorize finished for chromosome arm 4q 
winsorize finished for chromosome arm 5p 
winsorize finished for chromosome arm 5q 
winsorize finished for chromosome arm 6p 
winsorize finished for chromosome arm 6q 
winsorize finished for chromosome arm 7p 
winsorize finished for chromosome arm 7q 
winsorize finished for chromosome arm 8p 
winsorize finished for chromosome arm 8q 
winsorize finished for chromosome arm 9p 
winsorize finished for chromosome arm 9q 
winsorize finished for chromosome arm 10p 
winsorize finished for chromosome arm 10q 
winsorize finished for chromosome arm 11p 
winsorize finished for chromosome arm 11q 
winsorize finished for chromosome arm 12p 
winsorize finished for chromosome arm 12q 
winsorize finished for chromosome arm 13q 
winsorize finished for chromosome arm 14q 
winsorize finished for chromosome arm 15q 
winsorize finished for chromosome arm 16p 
winsorize finished for chromosome arm 16q 
winsorize finished for chromosome arm 17p 
winsorize finished for chromosome arm 17q 
winsorize finished for chromosome arm 18p 
winsorize finished for chromosome arm 18q 
winsorize finished for chromosome arm 19p 
winsorize finished for chromosome arm 19q 
winsorize finished for chromosome arm 20p 
winsorize finished for chromosome arm 20q 
winsorize finished for chromosome arm 21q 
winsorize finished for chromosome arm 22q 
winsorize finished for chromosome arm 23p 
winsorize finished for chromosome arm 23q 
> 
> #Use pcf to find segments:        
> uni.segments <- pcf(data=wins.data,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 
> 
> #Use multipcf to find segments as well:
> multi.segments <- multipcf(data=wins.data,gamma=12)
multipcf finished for chromosome arm 1p 
multipcf finished for chromosome arm 1q 
multipcf finished for chromosome arm 2p 
multipcf finished for chromosome arm 2q 
multipcf finished for chromosome arm 3p 
multipcf finished for chromosome arm 3q 
multipcf finished for chromosome arm 4p 
multipcf finished for chromosome arm 4q 
multipcf finished for chromosome arm 5p 
multipcf finished for chromosome arm 5q 
multipcf finished for chromosome arm 6p 
multipcf finished for chromosome arm 6q 
multipcf finished for chromosome arm 7p 
multipcf finished for chromosome arm 7q 
multipcf finished for chromosome arm 8p 
multipcf finished for chromosome arm 8q 
multipcf finished for chromosome arm 9p 
multipcf finished for chromosome arm 9q 
multipcf finished for chromosome arm 10p 
multipcf finished for chromosome arm 10q 
multipcf finished for chromosome arm 11p 
multipcf finished for chromosome arm 11q 
multipcf finished for chromosome arm 12p 
multipcf finished for chromosome arm 12q 
multipcf finished for chromosome arm 13q 
multipcf finished for chromosome arm 14q 
multipcf finished for chromosome arm 15q 
multipcf finished for chromosome arm 16p 
multipcf finished for chromosome arm 16q 
multipcf finished for chromosome arm 17p 
multipcf finished for chromosome arm 17q 
multipcf finished for chromosome arm 18p 
multipcf finished for chromosome arm 18q 
multipcf finished for chromosome arm 19p 
multipcf finished for chromosome arm 19q 
multipcf finished for chromosome arm 20p 
multipcf finished for chromosome arm 20q 
multipcf finished for chromosome arm 21q 
multipcf finished for chromosome arm 22q 
multipcf finished for chromosome arm 23p 
multipcf finished for chromosome arm 23q 
> 
> #Plot data and pcf-segments for one sample separately for each chromosome:
> plotSample(data=sub.lymphoma,segments=uni.segments,sample=1,layout=c(5,5))
> #Add cytoband text to ideogram (one page per chromosome to ensure sufficient 
> #space)
> plotSample(data=sub.lymphoma,segments=uni.segments,sample=1,layout=c(1,1),
+     cyto.text=TRUE)
> #Add multipcf-segmentation results, drop legend
> plotSample(data=sub.lymphoma,segments=list(uni.segments,multi.segments),sample=1,
+     layout=c(5,5),seg.col=c("red","blue"),seg.lwd=c(3,2),legend=FALSE)
> #Plot by chromosome for two samples, but only chromosome 1-9. One window per 
> #sample:
> plotSample(data=sub.lymphoma,segments=list(uni.segments,multi.segments),sample=
+     c(2,3),chrom=c(1:9),layout=c(3,3),seg.col=c("red","blue"),
+     seg.lwd=c(3,2),onefile=FALSE)
Error in dev.new(width = arg$plot.size[1], height = arg$plot.size[2],  : 
  no suitable unused file name for pdf()
Calls: plotSample -> dev.new
Execution halted


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