makePlot.gc {QoRTs}R Documentation

Plot GC content

Description

Plots GC content.

Usage

  makePlot.gc(plotter, plot.medians = NULL, plot.means = TRUE, 
              plotRate = FALSE, byPair = FALSE, useFQ = FALSE,
              debugMode, singleEndMode, 
              rasterize.plotting.area = FALSE, raster.height = 1000, raster.width = 1000,
              plot = TRUE,
              ...)

Arguments

plotter

A QoRT_Plotter reference object. See build.plotter.

plot.medians

A logical value indicating whether or not to plot the median average GC content for each bam file at the bottom of the plot. Overrides plot.means.

plot.means

A logical value indicating whether or not to plot the mean average GC content for each bam file at the bottom of the plot.

plotRate

A logical value indicating whether or not the X-axis should be the raw number of nucleotides that are G/C, vs the rate G/C.

byPair

Logical. If FALSE, GC content rates will be calculated for all reads individually. If TRUE, GC content rates will be calculated for all read-pairs. Note that when the insert size is small, the paired plot can sometimes appear jagged, as completely-overlapped read-pairs will always have an even number of G/C nucleotides.

useFQ

Logical. If TRUE, plot the G/C rate from the unaligned FASTQ data. This requires that the FASTQ data was supplied to QoRTs in the QoRTs QC step.

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: Percent of the read-pairs that is made up of G's or C's.

y-axis: Rate at which the given percent occurs.

See Also

build.plotter

Examples

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

## Starting: GC Content plot.

## Finished: GC Content plot.[time: 2018-09-25 13:12:27],[elapsed: 0.1 secs]

plot of chunk unnamed-chunk-1

[Package QoRTs version 1.3.6 Index]