An object of class TssData, TssNorm, or
TssResult.
y
A single integer or character string specifying which segment
to plot. An integer is interpreted as the index of the segment while
a character string is matched against the segment names.
...
Optional arguments used in order to customize the figure. See
the ‘details’ section.
Details
With the plot method, the raw, normalized, or final data can
easily be visualized.
The plot method uses a special system in order to customize the
graphical elements of the figure. It allows to refer to the different
components with the name of the additional input argument; its value
is a list containing named graphical parameters for the underlying
plot function. The following list describes the available names and
their contribution.
plot
Graphical parameters for the axes and the
labeling, passed to the plot function.
counts
Logical indicating whether the raw counts
should be plotted.
countsArgs
Graphical parameters for the
‘counts’ variable, passed to the points function.
ratio
Logical indicating whether the estimates based
on the Poisson ratios should be plotted.
ratioArgs
Graphical parameters for the
‘ratio’ variable, passed to the points function.
fit
Logical indicating whether the estimates based on
the fitting should be plotted.
fitArgs
Graphical parameters for the
‘fit’ variable, passed to the points function.
expect
Logical indicating whether the background
estimates should be plotted.
expectArgs
Graphical parameters for the
‘expect’ variable, passed to the points function.
expect
Logical indicating whether the background
estimates should be computed for all positions, rather than only
for those with reads.
tss
Logical indicating whether the identified TSS
should be plotted.
tssArgs
Graphical parameters for the
‘tss’ variable, passed to the points function.
threshold
Logical indicating whether the threshold parameter
used in the identification step should be indicated.
thresholdArgs
Graphical parameters for the
‘threshold’ variable, passed to the abline function.
rug
Logical indicating whether the location of the identified TSS
should be indicated.
rugArgs
Graphical parameters for the
‘rug’ variable, passed to the rug function.
baseline
Logical indicating whether a baseline
indicating zero reads should be drawn.
baselineArgs
Graphical parameters for the
‘baseline’ variable, passed to the abline function.
legend
Logical indicating whether a legend should be
plotted.
legendArgs
Graphical parameters for the
‘legend’ variable, passed to the legend function.
Thus, for (a) omitting the ratio estimates, the threshold, and the
legend, (b) customizing the graphical parameters of the raw read
counts, (c) customizing the axis labels and the title, the following
code can be used: