genomePlot {snapCGH} | R Documentation |
Basic plot of the log2 ratios for each array ordered along the genome.
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), ...)
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 |
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.
John Marioni