genomePlot: Plots the genome

In snapCGH: Segmentation, normalisation and processing of aCGH data

Description

Basic plot of the log2 ratios for each array ordered along the genome.

Usage

genomePlot(input, array = 1, naut = 22, Y = FALSE, X
                 = FALSE, main = NA, status, values, pch, cex, col, chrominfo =
                 chrominfo.Mb, ylim = c(-2, 2), ylb = "Log2Ratio",
                 chrom.to.plot = NA, xlim = c(0,NA), ...)

Arguments

input	an object of class MAList or SegList
array	integer of the array (sample) to be plotted.
naut	number of autosomes in the organism
Y	TRUE if chromosome Y is to be plotted, FALSE otherwise
X	TRUE if chromosome X is to be plotted, FALSE otherwise
main	Provides the title of the plot
status	character vector giving the control status of each spot on the array, of same length as the number of rows of log2ratios(input). If omitted, all points are plotted in the default color, symbol and size.
values	character vector giving values of status to be highlighted on the plot. Defaults to unique values of status. Ignored if there is no status vector.
pch	vector or list of plotting characters. Default to integer code 16. Ignored is there is no status vector.
col	numeric or character vector of colors, of the same length as values. Defaults to 1:length(values). Ignored if there is no status vector.
cex	numeric vector of plot symbol expansions, of the the same length as values. Defaults to 0.2 for the most common status value and 1 for the others. Ignored if there is no status vector.
chrominfo	a chromosomal information associated with the mapping of the data.
ylim	Minimum y-scale to use for plotting.
chrom.to.plot	Specify which chromosome to plot
ylb	label for the Y-axis.
xlim	limits for the x-axis
...	Any other parameters

Details

The status vector is intended to specify the control status of each spot, for example "gene", "ratio control", "house keeping gene", "buffer" and so on. The vector is usually computed using the function controlStatus and a spot-types file. However the function may be used to highlight any subset of spots.

Author(s)

John Marioni

See Also

MAList SegList

snapCGH documentation built on Nov. 8, 2020, 5:31 p.m.