R: Splice Junction Loci Count Plot

makePlot.splice.junction.loci.counts {QoRTs}

R Documentation

Splice Junction Loci Count Plot

Description

Plots the rate at which splice junction loci fall into various categories.

Usage

makePlot.splice.junction.loci.counts(plotter, 
                                 calc.rate = FALSE, 
                                 high.low.cutoff = 4,
                                 debugMode, singleEndMode, 
                                 plot = TRUE, ...)

Arguments

`plotter`	A `QoRT_Plotter` reference object. See `build.plotter`.
`calc.rate`	Logical. If TRUE, the proportion of loci in each category will be calculated and plotted, rather than the raw number.
`high.low.cutoff`	(For advanced users only!) The cutoff between "high" and "low" expression junction loci. Note that this must match the cutoff used by the jarfile QC execution.
`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

This function plots the number (y-axis) of splice junction loci of each type that appear in the bam-file's reads. Splice junctions are split into 4 groups, first by whether the splice junction appears in the transcript annotation gtf ("known" vs "novel"), and then by whether the splice junction has 4 or more reads covering it, or 1-3 reads ("Hi" vs "Lo").

Examples

  data(res,package="QoRTsExampleData");
  plotter <- build.plotter.colorByGroup(res);
  makePlot.splice.junction.loci.counts(plotter);

## Starting: Splice Junction Loci Rates plot.

## Finished: Splice Junction Loci Rates plot.[time: 2018-09-25 13:13:24],[elapsed: 0.08 secs]

  #Add a legend:
  makePlot.legend.over("topright", plotter)

plot of chunk unnamed-chunk-1