Arguments
sequence
character, Name of the sequence/chromosome of the region to
plot (for example "chr5" would be typical)
xlim
numeric of size 2, start and end position of the region
to plot
ylim
numeric of size 2, range for the y-axis
count.threshold
numeric, minimum number of reads in the reference set to
display a point in the plot
with.gene
logical, Should the gene information (obtained from
the annotation data) be plotted under the read depth plot?
col
character, Colour for the line displaying the read depth
ratio for each exon