Usage
cnSpec(x, y = NULL, genome = "hg19", plot_title = NULL, CN_Loss_colour = "#002EB8", CN_Gain_colour = "#A30000", x_title_size = 12, y_title_size = 12, facet_lab_size = 10, plotLayer = NULL, out = "plot", CNscale = "absolute")
Arguments
x
Object of class data frame with rows representing copy-number
segment calls. The data frame must contain columns with the following names
"chromosome", "start", "end", "segmean", "sample".
y
Object of class data frame with rows representing chromosome
boundaries for a genome assembly. The data frame must contain columns with
the following names "chromosome", "start", "end" (optional: see details).
genome
Character string specifying a valid UCSC genome (see details).
plot_title
Character string specifying title to display on the plot.
CN_Loss_colour
Character string specifying the colour value of copy
number losses.
CN_Gain_colour
Character string specifying the colour value of copy
number gains.
x_title_size
Integer specifying the size of the x-axis title.
y_title_size
Integer specifying the size of the y-axis title.
facet_lab_size
Integer specifying the size of the faceted labels
plotted.
plotLayer
Valid ggplot2 layer to be added to the plot.
out
Character vector specifying the the object to output, one of
"data", "grob", or "plot", defaults to "plot" (see returns).
CNscale
Character string specifying if copy number calls supplied are
relative (i.e.copy neutral == 0) or absolute (i.e. copy neutral ==2). One of
"relative" or "absolute"