plotSegmentedGenome {snapCGH} | R Documentation |
Basic plot of the log2 ratios for each array ordered along the genome.
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)
... |
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 |
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.
Mike Smith