Last data update: 2014.03.03

 R: Plot copy number data and/or segmentation results by...
plotChromR Documentation

Plot copy number data and/or segmentation results by chromosome

Description

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

Usage

plotChrom(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 copy number plots may be specified, see plotSample on these.

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

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

See Also

plotSample, 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.res <- winsorize(data=sub.lymphoma,return.outliers=TRUE)

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

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

#Plot data and segments for chromosome 1 separately for each sample:
plotChrom(data=sub.lymphoma,segments=list(uni.segments,multi.segments),chrom=1,
    layout=c(3,2))
#Let xaxis be probe index, and do not connect segments by vertical lines:
plotChrom(data=sub.lymphoma,segments=list(uni.segments,multi.segments),chrom=1,
    xaxis="index",layout=c(3,2),legend=FALSE,connect=FALSE)
#Data was winsorized earlier. Mark winsorized values by different color
#and symbol: 
plotChrom(data=wins.res,chrom=1,winsoutliers=wins.res,layout=c(3,2))
#Save plots in working directory:
plotChrom(data=sub.lymphoma,segments=uni.segments,chrom=c(1,2),
    layout=c(3,2),dir.print=getwd(),file.name=c("chromosome1","chromosome2"),
    onefile=FALSE)

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/plotChrom.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotChrom
> ### Title: Plot copy number data and/or segmentation results by chromosome
> ### Aliases: plotChrom
> 
> ### ** 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.res <- winsorize(data=sub.lymphoma,return.outliers=TRUE)
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.res,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.res,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 segments for chromosome 1 separately for each sample:
> plotChrom(data=sub.lymphoma,segments=list(uni.segments,multi.segments),chrom=1,
+     layout=c(3,2))
> #Let xaxis be probe index, and do not connect segments by vertical lines:
> plotChrom(data=sub.lymphoma,segments=list(uni.segments,multi.segments),chrom=1,
+     xaxis="index",layout=c(3,2),legend=FALSE,connect=FALSE)
> #Data was winsorized earlier. Mark winsorized values by different color
> #and symbol: 
> plotChrom(data=wins.res,chrom=1,winsoutliers=wins.res,layout=c(3,2))
> #Save plots in working directory:
> ## No test: 
> plotChrom(data=sub.lymphoma,segments=uni.segments,chrom=c(1,2),
+     layout=c(3,2),dir.print=getwd(),file.name=c("chromosome1","chromosome2"),
+     onefile=FALSE)
Plot was saved in  /home/ddbj/DataUpdator-rgm3/target/chromosome1.pdf 
Plot was saved in  /home/ddbj/DataUpdator-rgm3/target/chromosome2.pdf 
> ## End(No test)  
> 
> 
> 
> 
> 
> dev.off()
Error in dev.off() : cannot shut down device 1 (the null device)
Execution halted


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