R: Clipped sequence nucleotide-by-position plot

makePlot.NVC.lead.clip {QoRTs}

R Documentation

Clipped sequence nucleotide-by-position plot

Description

Plots the nucleotide rates for clipped segments

Usage

makePlot.NVC.lead.clip(plotter, clip.amt,  r2.buffer, 
                   points.highlighted = TRUE,
                   label.majority.bases = TRUE, 
                   label.majority.bases.threshold = 0.5, 
                   label.majority.bases.cex = 1, 
                   rasterize.plotting.area = FALSE, 
                   raster.height = 1000, 
                   raster.width = 1000,
                   show.base.legend = TRUE, 
                   debugMode, singleEndMode,
                   ...)


makePlot.NVC.tail.clip(plotter, clip.amt,  r2.buffer, 
                       points.highlighted = TRUE, 
                       label.majority.bases = TRUE, 
                       label.majority.bases.threshold = 0.5, 
                       label.majority.bases.cex = 1, 
                       rasterize.plotting.area = FALSE, 
                       raster.height = 1000, 
                       raster.width = 1000,
                       show.base.legend = TRUE, 
                       debugMode, singleEndMode, ...)

Arguments

`plotter`	A `QoRT_Plotter` reference object. See `build.plotter`.
`clip.amt`	Numeric value. The number of bases clipped. These methods only plot the sequence for a single specific clip.amt.
`r2.buffer`	Buffer space to place between the plotting of read 1 and read 2. By default this will choose a reasonable value.
`points.highlighted`	A logical value. Determines whether to ever plot points on top of the lines. This can be useful for identifying outliers. If TRUE, then all highlighted lane-bams will be overlaid with points using their designated pch symbol. If the plotter does not highlight any lanebams, then points will be overlaid on ALL lines.
`label.majority.bases`	A logical value indicating whether to label the genotypes of read cycles in which the most common base has a frequency exceeding label.majority.bases.threshold (see below).
`label.majority.bases.threshold`	A numeric value indicating the cutoff above which the most common base will be labelled, if label.majority.bases is set TRUE (see above).
`label.majority.bases.cex`	The cex value fed to text() that is used to determine how big the labels are to be, if label.majority.bases is TRUE. (see `par` for information on cex).
`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.
`show.base.legend`	A logical value indicating whether to print the base-color legend along the right edge of the plot.
`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.
`...`	Arguments to be passed to methods, such as graphical parameters (see `par`).

Details

For general information on reading NVC plots, see makePlot.NVC.

This function plots the nucleotide rates for the sections of reads that were soft-clipped by the aligner. Note that these will not function on reads that have been aligned using an aligner that does not practice soft clipping (such as TopHat2).

Examples

  data(res,package="QoRTsExampleData");
  plotter <- build.plotter.colorByGroup(res);
  makePlot.NVC.lead.clip(plotter, clip.amt = 12);

## Starting: Lead Clipping NVC plot.
## Finished: Lead Clipping NVC plot.[time: 2016-01-28 16:32:49],[elapsed: 0.33 secs]

plot of chunk unnamed-chunk-1

  makePlot.NVC.tail.clip(plotter, clip.amt = 12);

## Starting: Tail Clipping NVC plot.
## Finished: Tail Clipping NVC plot.[time: 2016-01-28 16:32:49],[elapsed: 0.39 secs]