plotSample: Plot the data and results from segmentation for a single...
In DNAcopy: DNA copy number data analysis

Description Usage Arguments Details Examples

Plots the data for a single sample from a copy number array experiment (aCGH, ROMA etc.) along with the results of segmenting it into regions of equal copy numbers.

  plotSample(x, sampleid=NULL, chromlist=NULL, xmaploc=FALSE,
             col=c("black","green"), pch=".", cex=NULL, altcol=TRUE,
             segcol="red", lwd=3, zeroline=TRUE, zlcol="grey",
             xlab=NULL, ylab=NULL, main=NULL, ...)

`x`	an object of class `DNAcopy` resulting from analyzing data from copy number array experiments.
`sampleid`	the sample for which the plot is requested. Should be a valid sample name or number. If missing the first sample is plotted.
`chromlist`	a vector of chromosome numers or names to be plotted. If missing the whole genome is plotted.
`xmaploc`	a logical indicating if data are plotted against genomic position or Index. Defaults to `FALSE`.
`col`	a vector of two colors that can be used for alternating colors for successive chromosomes.
`pch`	the plotting character. Defaults to `.`.
`cex`	the size of plotting character. If missing it is set to 3 if pch is ‘.’ and 1 otherwise.
`altcol`	a logical indicating if colors of successive chromosomes should be alternated. Defaults to `TRUE`.
`segcol`	color for segment means.
`zeroline`	a logical indicating if the zeroline is drawn. Defaults to `TRUE`.
`zlcol`	color for zero line.
`lwd`	thickness of the lines.
`xlab`	the x-axis lavel. If missing Index or Genomic Position will be used depending on xmaploc.
`ylab`	the y-axis label. If missing log(CN) or LOH will be used depending on data type.
`main`	the main title. If missing sample name will be used.
`...`	other arguments to the `plot` function can be passed here.

This function plots the whole genome and segmentation results for a single sample. This function overcomes the deficiency in the plot.DNAcopy function which cycles through all the samples. If sampleid is not specified the first sample is plotted.

#Read in two examples from Snijders et al.

data(coriell)

#Combine into one CNA object to prepare for analysis on Chromosomes 1-23

CNA.object <- CNA(cbind(coriell$Coriell.05296,coriell$Coriell.13330),
                  coriell$Chromosome,coriell$Position,
                  data.type="logratio",sampleid=c("c05296","c13330"))

#We generally recommend smoothing single point outliers before analysis
#Make sure to check that the smoothing is proper

smoothed.CNA.object <- smooth.CNA(CNA.object)

#Segmentation at default parameters

segment.smoothed.CNA.object <- segment(smoothed.CNA.object, verbose=1)

# Plot whole sample c13330

plotSample(segment.smoothed.CNA.object, sampleid="c13330")

# Plot only chromosomes 1,3,5,7,9 from first sample
plotSample(segment.smoothed.CNA.object, sampleid=1, chromlist=c(1,3,5,7,9))