Usage
lohView(x, y = NULL, genome = "hg19", chr = "chr1", ideogram_txtAngle = 45, ideogram_txtSize = 5, plotLayer = NULL, ideogramLayer = NULL, out = "plot")
Arguments
x
object of class data frame with rows representing Heterozygous
Germline calls. The data frame must contain columns with the following names
"chromosome", "position", "n_vaf", "t_vaf", "sample".
y
Object of class data frame with rows representing cytogenetic bands
for a chromosome. The data frame must contain columns with the following
names "chrom", "chromStart", "chromEnd", "name", "gieStain" for plotting the
ideogram (optional: see details).
genome
Character string specifying a valid UCSC genome (see details).
chr
Character string specifying which chromosome to plot one of
"chr..." or "all"
ideogram_txtAngle
Integer specifying the angle of cytogenetic labels
on the ideogram subplot.
ideogram_txtSize
Integer specifying the size of cytogenetic labels on
the ideogram subplot.
plotLayer
Valid ggplot2 layer to be added to the copy number plot.
ideogramLayer
Valid ggplot2 layer to be added to the ideogram
sub-plot.
out
Character vector specifying the the object to output, one of
"data", "grob", or "plot", defaults to "plot" (see returns).