plotSegmentedGenome {snapCGH}R Documentation

Plots the genome

Description

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

Usage

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

Arguments

... Objects of class 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
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
colors vector of colors to plot segmented states of each SegList passed to the function.
mark.regions Boolean. If true will colour code the segmentation plot using the information stored in $regions and generated by nudSegmentation, or an equivalent method.
main Specify the title of the plot

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)

Mike Smith

See Also

genomePlot SegList

Examples



[Package snapCGH version 1.4.0 Index]