makePlot.cigarOp.byCycle {QoRTs}R Documentation

Plot Cigar Operator Rate

Description

Plots the rate at which the given CIGAR operator occurs, by read cycle.

Usage

  makePlot.cigarOp.byCycle(plotter, 
           op=c("SoftClip","Del","Ins","HardClip","Pad","Splice","Aln"), 
           r2.buffer = NULL, 
           rate.per.million = TRUE, 
           use.readLength.denominator = TRUE, 
           debugMode, 
           singleEndMode,
           rasterize.plotting.area = FALSE, 
           raster.height = 1000, 
           raster.width = 1000,
           plot = TRUE,
           ...)

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.

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.

use.readLength.denominator

Logical. If TRUE, use the read-length counts as the denominator when calculating op rates. This is only relevant if operating on trimmed reads, where the read length is variable.

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.

rasterize.plotting.area

Logical. If TRUE, then "flatten" the plotting lines into a raster format. This requires support for png file creation and the installation of the "png" package. Only the plotting lines will be rasterized, the axes and annotations will be vector format. Default is FALSE.

raster.height

Numeric integer. If rasterize.plotting.area is TRUE, then this will set the height of the rasterized plot, in pixels.

raster.width

Numeric integer. If rasterize.plotting.area is TRUE, then this will set the width of the rasterized plot, in pixels.

plot

Logical. If FALSE, suppress plotting and return TRUE if and only if the data is present in the dataset to allow plotting. Useful to automatically filter out missing data plots.

...

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.

See Also

build.plotter

Examples

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

## Starting: Deletion Rate, by read cycle plot.

## Finished: Deletion Rate, by read cycle plot.[time: 2018-09-25 13:12:17],[elapsed: 0.29 secs]

plot of chunk unnamed-chunk-1

  makePlot.cigarOp.byCycle(plotter, op = "Ins");

## Starting: Insertion Rate, by read cycle plot.

## Finished: Insertion Rate, by read cycle plot.[time: 2018-09-25 13:12:18],[elapsed: 0.34 secs]

plot of chunk unnamed-chunk-1

  makePlot.cigarOp.byCycle(plotter, op = "Splice");

## Starting: Splice Junction Rate, by read cycle plot.

## Finished: Splice Junction Rate, by read cycle plot.[time: 2018-09-25 13:12:18],[elapsed: 0.37 secs]

plot of chunk unnamed-chunk-1

[Package QoRTs version 1.3.6 Index]