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
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
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 bayesCGH::nudSegmentation, or an equivalent method.
main
Specify the title of the plot