segPlot: Plots the data from a copy number array experiment (aCGH,...
In fastseg: fastseg - a fast segmentation algorithm

Description Usage Arguments Value Author(s) Examples

View source: R/segPlot.R

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

  segPlot(x, res, plot.type = "chrombysample",
    altcol = TRUE, sbyc.layout = NULL, cbys.nchrom = 1,
    cbys.layout = NULL, include.means = TRUE,
    zeroline = TRUE, pt.pch = NULL, pt.cex = NULL,
    pt.cols = NULL, segcol = NULL, zlcol = NULL,
    ylim = NULL, lwd = NULL, ...)

`x`	The object that was segmented by fastseg.
`res`	The result of fastseg.
`plot.type`	the type of plot. (Default = "s").
`altcol`	logical flag to indicate if chromosomes should be plotted in alternating colors in the whole genome plot. (Default = TRUE).
`sbyc.layout`	`layout` settings for the multifigure grid layout for the ‘samplebychrom’ type. It should be specified as a vector of two integers which are the number of rows and columns. The default values are chosen based on the number of chromosomes to produce a near square graph. For normal genome it is 4x6 (24 chromosomes) plotted by rows. (Default = NULL).
`cbys.layout`	`layout` settings for the multifigure grid layout for the ‘chrombysample’ type. As above it should be specified as number of rows and columns and the default chosen based on the number of samples. (Default = NULL).
`cbys.nchrom`	the number of chromosomes per page in the layout. (Default = 1).
`include.means`	logical flag to indicate whether segment means are to be drawn. (Default = TRUE).
`zeroline`	logical flag to indicate whether a horizontal line at y=0 is to be drawn. (Default = TRUE).
`pt.pch`	the plotting character used for plotting the log-ratio values. (Default = ".")
`pt.cex`	the size of plotting character used for the log-ratio values (Default = 3).
`pt.cols`	the color list for the points. The colors alternate between chromosomes. (Default = c("green","black").
`segcol`	the color of the lines indicating the segment means. (Default = "red").
`zlcol`	the color of the zeroline. (Default = "grey").
`ylim`	this argument is present to override the default limits which is the range of symmetrized log-ratios. (Default = NULL).
`lwd`	line weight of lines for segment mean and zeroline. (Default = 3).
`...`	other arguments which will be passed to `plot` commands.

A plot of the values and segments.

klambaue

data(coriell)
head(coriell)
samplenames <- colnames(coriell)[4:5]
data <- as.matrix(coriell[4:5])
chrom <- coriell$Chromosome
maploc <- coriell$Position
library("GenomicRanges")
gr <- GRanges(seqnames=chrom,
		ranges=IRanges(maploc, end=maploc))
mcols(gr) <- data
colnames(mcols(gr)) <- samplenames
res <- fastseg(gr)
segPlot(gr,res)

Loading required package: GenomicRanges
Loading required package: stats4
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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
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    'browseVignettes()'. To cite Bioconductor, see
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        Clone Chromosome Position Coriell.05296 Coriell.13330
1  GS1-232B23          1        1      0.000359      0.207470
2  RP11-82d16          1      469      0.008824      0.063076
3  RP11-62m23          1     2242     -0.000890      0.123881
4  RP11-60j11          1     4505      0.075875      0.154343
5 RP11-111O05          1     5441      0.017303     -0.043890
6  RP11-51b04          1     7001     -0.006770      0.094144