segPlot {fastseg} | R Documentation |
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 |
|
cbys.layout |
|
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
|
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)