R: Chromosome type rate plot

makePlot.chrom.type.rates {QoRTs}

R Documentation

Chromosome type rate plot

Description

Plots the number or percent of read-pairs falling on each type of chromosome.

Usage

makePlot.chrom.type.rates(plotter, 
                      plot.rates = TRUE,
                      chromosome.name.style = "UCSC",
                      exclude.autosomes = FALSE,
                      chrom.norm.factors = NULL,
                      custom.chromosome.style.def.function = NULL,
                      return.table = FALSE, 
                      debugMode, singleEndMode,
                      plot = TRUE,
                      ...)

Arguments

`plotter`	A `QoRT_Plotter` reference object. See `build.plotter`.
`plot.rates`	A logical value indicating whether to plot percent of the total (for each bam file), rather than read-counts.
`chromosome.name.style`	A string value indicating the style of the chromosome names, and also how to split up the categories. There are 4 legal options: "UCSC": The default. Chromosomes are named: "chr1,chr2,...,chrX,chrY,chrXY,chrM". There are 6 categories: autosome, X, Y, XY, mitochondrial, and other. "ENSEMBL": Chromosomes are named: "1,2,...,X,Y,XY,MT". There are 6 categories: autosome, X, Y, XY, mitochondrial, and other. "UCSC_WITH_ERCC": As UCSC, but there is an additional category, which contains all chromosomes that begin with the text "ERCC". "ENSEMBL_WITH_ERCC": As ENSEMBL, but there is an additional category, which contains all chromosomes that begin with the text "ERCC".
`chrom.norm.factors`	(Advanced users)
`exclude.autosomes`	A logical value indicating whether to exclude autosomes from the plot.
`custom.chromosome.style.def.function`	(For advanced users) If your chromosomes do not match any of the above styles, then you can set your own chromosome style by handing this option a function. The function must take one argument. When handed NULL, it must return a list of all legal categories. When handed a single chromosome name, it must return one of those categories.
`return.table`	A Logical value. If TRUE, the function will return a table containing the plotted data.
`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 read-pairs mapping to each category of chromosome.

Value

By default, this function returns nothing. If the return.table parameter is TRUE, then it returns a data.frame with the data that was plotted.

Examples

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

## Starting: Chromosome Rates plot.

## Finished: Chromosome Rates plot.[time: 2018-09-25 13:12:11],[elapsed: 0.2 secs]

plot of chunk unnamed-chunk-1

[Package QoRTs version 1.3.6 Index]