| makePlot.gc {QoRTs} | R Documentation |
Plots GC content.
makePlot.gc(plotter, plot.medians = NULL, plot.means = TRUE,
plotRate = FALSE, byPair = FALSE,
debugMode, singleEndMode, ...)
plotter |
A |
plot.medians |
A logical value indicating whether or not to plot the median
average GC content for each bam file at the bottom
of the plot. Overrides |
plot.means |
A logical value indicating whether or not to plot the mean average GC content for each bam file at the bottom of the plot. |
plotRate |
A logical value indicating whether or not the X-axis should be the raw number of nucleotides that are G/C, vs the rate G/C. |
byPair |
Logical. If FALSE, GC content rates will be calculated for all reads individually. If TRUE, GC content rates will be calculated for all read-pairs. Note that when the insert size is small, the paired plot can sometimes appear jagged, as completely-overlapped read-pairs will always have an even number of G/C nucleotides. |
debugMode |
Logical. If TRUE, debugging data will be printed to the console. |
singleEndMode |
Logical. Determines whether the dataset consists of single-ended reads. By default this is determined from the data. Thus, this parameter should never need to be set by the user. |
... |
Arguments to be passed to methods, such as
graphical parameters (see |
x-axis: Percent of the read-pairs that is made up of G's or C's.
y-axis: Rate at which the given percent occurs.
data(res,package="QoRTsExampleData");
plotter <- build.plotter.colorByGroup(res);
makePlot.gc(plotter)
## Starting: GC Content plot.
## Finished: GC Content plot.[time: 2016-01-28 16:32:56],[elapsed: 0.06 secs]