R: Plot the length distribution of a given cigar operation

makePlot.cigarLength.distribution {QoRTs}

R Documentation

Plot the length distribution of a given cigar operation

Description

Plots the length distribution of a given cigar operation

Usage

  makePlot.cigarLength.distribution(plotter, op, 
                                r2.buffer = NULL,
                                perMillion = TRUE,
                                log.x = FALSE, 
                                log.y = FALSE, 
                                debugMode, singleEndMode,
                                ...)

Arguments

`plotter`	A `QoRT_Plotter` reference object. See `build.plotter`.
`op`	A character string naming which cigar op to plot. Must be one of the following: `"SoftClip"` Soft Clip (Cigar Op "S") `"HardClip"` Hard Clip (Cigar Op "H") `"Del"` Deletion from reference (Cigar Op "D") `"Ins"` Insertion from reference (Cigar Op "I") `"Pad"` Padding (Cigar Op "P") `"Splice"` Splice Junction (Cigar Op "N") `"Aln"` Aligned to reference (Cigar Op "M") Note that makePlot.cigarOp.byCycle(plotter,"SoftClip") gives identical results as makePlot.clipping, although the default value for the `rate.per.million` argument is different.
`r2.buffer`	Buffer space to place between the plotting of read 1 and read 2. By default this will choose a reasonable value.
`perMillion`	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.
`log.x`	A logical value indicating whether or not to log-scale the x axis.
`log.y`	A logical value indicating whether or not to log-scale the y axis.
`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: Length of the cigar operation.

y-axis: Frequency of the given length.

Examples

  data(res,package="QoRTsExampleData");
  plotter <- build.plotter.colorByGroup(res);
  makePlot.cigarLength.distribution(plotter, op = "Del");

## Starting: Deletion Length Distribution plot.
## Finished: Deletion Length Distribution plot.[time: 2016-01-28 16:32:53],[elapsed: 0.08 secs]

plot of chunk unnamed-chunk-1

  makePlot.cigarLength.distribution(plotter, op = "Ins");

## Starting: Insertion Length Distribution plot.
## Finished: Insertion Length Distribution plot.[time: 2016-01-28 16:32:53],[elapsed: 0.12 secs]