R: On-Target Rates

makePlot.onTarget {QoRTs}

R Documentation

On-Target Rates

Description

On-Target Rates.

Usage

makePlot.targetDistribution(plotter,
       plot.rates = TRUE, 
       plot.hist = TRUE, 
       log.y = TRUE, 
       singleEndMode,
       byPair = !singleEndMode, 
       rasterize.plotting.area = FALSE, 
       raster.height = 1000, 
       raster.width = 1000,
       debugMode,
       plot = TRUE,
       ...)

makePlot.onTarget.counts(plotter, 
      y.counts.in.millions = TRUE, 
      debugMode, 
      singleEndMode,
      plot = TRUE, ...)

makePlot.onTarget.rates(plotter,  
      debugMode, 
      singleEndMode,
      plot = TRUE, ...)

Arguments

`plotter`	A `QoRT_Plotter` reference object. See `build.plotter`.
`y.counts.in.millions`	Logical. If TRUE, y axis labels are labelled in millions.
`plot.rates`	Logical. If TRUE, plot rates, otherwise plot raw counts.
`plot.hist`	Plot a histogram.
`log.y`	Logical. If TRUE, the y-axis should be log-scaled.
`byPair`	Logical. If TRUE, count read-pairs rather than reads. In other words, if two reads overlap, the overlapping region is counted only once.
`rasterize.plotting.area`	Logical. If `TRUE`, the plotting area will be written to a temp png file then drawn to the current device as a raster image. This option is generally preferred for vector devices, because NVC plots can be very large when drawn in vector format. Note: this requires the `png` package!
`raster.height`	Numeric. If rasterize.plotting.area is TRUE, then this is the height of the plotting area raster image, in pixels.
`raster.width`	Numeric. If rasterize.plotting.area is TRUE, then this is the width of the plotting area raster image, in pixels.
`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, indicates the amount of time spent running the QoRTs QC data processing tool

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.runTimePerformance(plotter);

## Starting: QoRTs Runtime Performance plot.

## Finished: QoRTs Runtime Performance plot.[time: 2018-09-25 13:12:52],[elapsed: 0.13 secs]

plot of chunk unnamed-chunk-1

[Package QoRTs version 1.3.6 Index]