plotSegmentationDots {tilingArray} | R Documentation

## 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.

### Author(s)

Wolfgang Huber <huber@ebi.ac.uk>

[Package tilingArray version 1.66.0 Index]