| makePlot.qual.pair {QoRTs} | R Documentation |
Plots the Phred quality score as a function of the read cycle for both reads.
makePlot.qual.pair(plotter, y.name, r2.buffer = NULL,
debugMode, singleEndMode, ...)
plotter |
A |
y.name |
The name of the quality score metric to plot. Must be one of:
|
r2.buffer |
Buffer space to place between the plotting of read 1 and read 2. By default this will choose a reasonable value. |
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 |
These plots display information about the phred quality score (y-axis) as a function of the position in the read (x-axis). Five statistics can be plotted: minimum, maximum, upper and lower quartiles, and median. These statistics are calculated individually for each bam file and each read position (ie, each plotted line corresponds to a bam file).
Note that the Phred score is always an integer, and as such these plots would normally be very difficult to read because lines would be plotted directly on top of one another. To reduce this problem, the lines are vertically offset from one another. Most plotters offset each line by lane.ID.
data(res,package="QoRTsExampleData");
plotter <- build.plotter.colorByGroup(res);
makePlot.qual.pair(plotter,y.name="min");
## Starting: Minimum plot.
## Finished: Minimum Phred Quality Score plot.[time: 2016-01-28 16:33:04],[elapsed: 0.1 secs]
makePlot.qual.pair(plotter,y.name="median");
## Starting: Median plot.
## Finished: Median Phred Quality Score plot.[time: 2016-01-28 16:33:04],[elapsed: 0.13 secs]
makePlot.qual.pair(plotter,y.name="max");
## Starting: Maximum plot.
## Finished: Maximum Phred Quality Score plot.[time: 2016-01-28 16:33:04],[elapsed: 0.13 secs]
