tilingArray (version 1.50.0)

plotSegmentationDots: Plot points for a region along a chromosome

Description

Plot points for a region along a chromosome

Usage

plotSegmentationDots(dat, xlim, ylim, ylab, threshold=NA,  chr=1, strand="+", vpr, colors, main,  pointSize=unit(0.6, "mm"), showConfidenceIntervals=TRUE,  sepPlots=FALSE, cexAxisLabel=1, cexAxis=1,...)

Arguments

dat

list containing data to be plotted (see Details section below for particulars).

xlim

integer vector of length 2 with start and end coordinates (in bases) for plotting.

ylim

numeric vector containing the y limits of the plot.

ylab

character scalar (if sepPlots=FALSE) or vector containing y-axis label(s).

threshold

numeric scalar indicating the threshold of expression (default value is NA, for no threshold. If a value is supplied, it is subtracted from the intensity measures in dat$y.

chr

integer of length 1 indicating the chromosome to be plot (defaults to 1).

strand

character scalar which should be set to either + or - to indicate which strand of DNA to plot the intensity values from (defaults to "+").

vpr

which viewport to plot the figure in. If this function is called directly by the user this argument should be left missing.

colors

named character vector, optional. If missing, a default color scheme is used: c("+"="#00441b", "-"="#081d58", "duplicated"="grey", "cp"="#101010", "highlight"="red", "threshold"="grey"), where the first three elements refer to the colors of data points and the last three to the colors of lines in the plot.

main

character vector specifying plot title.

pointSize

an object of class unit which specifies the size of each point. Default value is unit(0.6, "mm").

showConfidenceIntervals

logical scalar indicating whether confidence intervals for each change-point are to be plotted (only available once segmentation has occurred).

sepPlots

logical scalar indicating whether the intensities are plotted separately for each array (if dat$y has multiple columns). Defaults to FALSE, in which case the average intensity for each probe is plotted. When TRUE, up to 3 arrays can be plotted separately (more than 3 gets crowded).

cexAxisLabel

numeric scalar specifying the magnification to be used for the y-axis label relative to the current test size.

cexAxis

numeric scalar specifying the magnification to be used for the y-axis annotation relative to the current text size.

...

additional arguments.

Details

This function is called by plotAlongChrom when the argument what is set to dots. Although this function can be called directly by the user, this is not recommended.

The dat list contains the following items: items x: x-coordinates (in bases) along chromosome,

1. y: intensity matrix of probes along chromosome,
2. flag: indicates probe uniqueness in the genome. Possibilities are 3: multiple perfect matches, 2: has no PM but one or more near-matches, 1: has exactly one PM and some near-matches in the genome, 0: has exactly one PM and no near-matches.
3. extras: (optional) matrix of additional values (such as test-statistics/p-values) to be plotted.