makePlot.qual.pair {QoRTs}R Documentation

Plot quality score by read cycle

Description

Plots the Phred quality score as a function of the read cycle for both reads.

Usage

  makePlot.qual.pair(plotter, y.name, r2.buffer = NULL, 
                 debugMode, singleEndMode, 
                 rasterize.plotting.area = FALSE, raster.height = 1000, raster.width = 1000,
                 plot = TRUE,
                 ...)

Arguments

plotter

A QoRT_Plotter reference object. See build.plotter.

y.name

The name of the quality score metric to plot. Must be one of:

  • "min"

  • "lowerQuartile"

  • "median"

  • "upperQuartile"

  • "max"

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.

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

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.

See Also

build.plotter

Examples

  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: 2018-09-25 13:13:00],[elapsed: 0.17 secs]

plot of chunk unnamed-chunk-1

  makePlot.qual.pair(plotter,y.name="median");

## Starting: Median plot.

## Finished: Median Phred Quality Score plot.[time: 2018-09-25 13:13:01],[elapsed: 0.27 secs]

plot of chunk unnamed-chunk-1

  makePlot.qual.pair(plotter,y.name="max");

## Starting: Maximum plot.

## Finished: Maximum Phred Quality Score plot.[time: 2018-09-25 13:13:01],[elapsed: 0.2 secs]

plot of chunk unnamed-chunk-1

  #Legend:
  makePlot.legend.box(plotter);

plot of chunk unnamed-chunk-1

[Package QoRTs version 1.3.6 Index]