R: Plot Alignment Clipping

makePlot.clipping {QoRTs}

R Documentation

Plot Alignment Clipping

Description

Plots the rate at which the aligner soft-clips off portions of aligned reads.

Usage

  makePlot.clipping(plotter, rate.per.million = FALSE, 
                r2.buffer = NULL, 
                debugMode, singleEndMode,
                ...)

Arguments

`plotter`	A `QoRT_Plotter` reference object. See `build.plotter`.
`rate.per.million`	A logical value indicating whether or not to scale the y axis to rate-per-million-reads, rather than rate-per-read. Some people may find the results more readable this way, even though the plots themselves will appear the same.
`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 `par`).

Details

x-axis: The read cycle (ie. the base-pair position in the read).

y-axis: The rate at which the bases at the given read-cycle is clipped off.

Examples

  data(res,package="QoRTsExampleData");
  plotter <- build.plotter.colorByGroup(res);
  makePlot.clipping(plotter)

## Starting: Alignment Clipping Rate, by read cycle plot.
## Finished: Alignment Clipping Rate, by read cycle plot.[time: 2016-01-28 16:32:55],[elapsed: 0.13 secs]

plot of chunk unnamed-chunk-1