R: Plot mapping rates

makePlot.mapping.rates {QoRTs}

R Documentation

Plot mapping rates

Description

Plots the rates at which reads map to the genome.

Usage

makePlot.mapping.rates(plotter, plot.mm = NULL, 
                   y.counts.in.millions = TRUE, 
                   debugMode, singleEndMode,
                   plot = TRUE,
                   ...)

Arguments

`plotter`	A `QoRT_Plotter` reference object. See `build.plotter`.
`plot.mm`	Plot multi-mapping rates. By default, it autodetects whether multimapping data was included in the original decoder.
`y.counts.in.millions`	Label/scale the y-axis in millions of reads.
`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.
`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

For each sample-run, this function plots the number of mapped reads and the rate at which reads map (if the total reads is provided).

Examples

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

## Starting: Mapping Rates plot.

## Finished: Mapping Rates plot.[time: 2018-09-25 13:12:44],[elapsed: 0.13 secs]

plot of chunk unnamed-chunk-1