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PSCBS (version 0.23.0)

plotTracks.PairedPSCBS: Plots parental specific copy numbers along the genome

Description

Plots parental specific copy numbers along the genome for one or more chromosomes. It is possible to specify what type of tracks to plot. Each type of track is plotted in its own panel.

Usage

## S3 method for class 'PairedPSCBS':
plotTracks(x, tracks=c("tcn", "dh", "tcn,c1,c2", "tcn,c1", "tcn,c2", "c1,c2", "betaN", "betaT", "betaTN")[1:3], scatter="*", calls=".*", pch=".", col=NULL, cex=1, changepoints=FALSE, grid=FALSE, quantiles=c(0.05, 0.95), xlim=NULL, Clim=c(0, 6), Blim=c(0, 1), xScale=1e-06, ..., add=FALSE, subplots=!add && (length(tracks) > 1), verbose=FALSE)

Arguments

x
A result object returned by segmentByPairedPSCBS().
tracks
A character vector specifying what types of tracks to plot.
scatter
A character vector specifying which of the tracks should have scatter plot.
calls
A character vector of regular expression identifying call labels to be highlighted in the panels.
pch
The type of the scatter points, if any.
col
The color of the scatter points, if any.
cex
The size of the scatter points, if any.
changepoints
If TRUE, changepoints are drawn as vertical lines.
grid
If TRUE, horizontal lines are displayed.
quantiles
A numeric vector in [0,1] specifying the quantiles of the confidence bands to be drawn, if any.
xlim
(Optional) The genomic range to plot.
Clim
The range of copy numbers.
Blim
The range of allele B fractions (BAFs) and decrease of heterozygosity (DHs).
xScale
The scale factor used for genomic positions.
...
Not used.
add
If TRUE, the panels plotted are added to the existing plot, otherwise a new plot is created.
subplots
If TRUE, then subplots are automatically setup.
verbose
See Verbose.

Value

  • Returns nothing.