R: Plot Biotype rates

makePlot.biotype.rates {QoRTs}

R Documentation

Plot Biotype rates

Description

Plots counts for each gene biotype. This plot is only useful and informative when QoRTs is run on a GTF file that contains "gene_biotype" tags.

Usage

  makePlot.biotype.rates(plotter, 
              plot.rates = TRUE,
              count.type = c("all","unambigOnly"),
              log.y = TRUE,
              return.table = FALSE, 
              debugMode = DEFAULTDEBUGMODE,  
              singleEndMode = plotter$res@singleEnd,
              showTypes,
              plot = TRUE,
              ...)

Arguments

`plotter`	A `QoRT_Plotter` reference object. See `build.plotter`.
`plot.rates`	A logical value. If `TRUE`, then reads/read-pairs per million should be plotted, rather than raw counts. Default is `TRUE`.
`count.type`	A logical value. If `TRUE`, then both ambiguous and unambiguous reads will be counted. Otherwise only unambiguous reads will be counted.
`log.y`	A logical value indicating that the y-axis should be log-scaled.
`return.table`	Logical. If `TRUE`, then return a data table.
`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.
`showTypes`	Character vector. An optional list of biotypes to include in the plot. By default all observed biotypes will be plotted.
`plot`	Logical. Default is `TRUE`. If `FALSE`, then do NOT plot any results, instead just return a data table.
`...`	Arguments to be passed to methods, such as graphical parameters (see `par`).

Details

x-axis: Gene "BioTypes", from the annotation GTF.

y-axis: Total read counts across all genes in the BioType, measured either in reads or reads-per-million.

Examples

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

## Starting: Biotype Rates plot.

## Finished: Biotype Rates plot.[time: 2018-09-25 13:12:08],[elapsed: 0.15 secs]

plot of chunk unnamed-chunk-1