R: Nucleotide-rate by read cycle plot

makePlot.raw.NVC {QoRTs}

R Documentation

Nucleotide-rate by read cycle plot

Description

Plots the nucleotide rate by read cycle

Usage

makePlot.raw.NVC(plotter,  r2.buffer = NULL, 
                         points.highlighted = TRUE,
                         label.majority.bases = FALSE, 
                         label.majority.bases.threshold = 0.5, 
                         label.majority.bases.cex = 0.5, 
                         rasterize.plotting.area = FALSE, 
                         raster.height = 1000, 
                         raster.width = 2000,
                         show.base.legend = TRUE, 
                         debugMode, singleEndMode,
                         ...)
                         
makePlot.minus.clipping.NVC(plotter,  r2.buffer = NULL, 
                         points.highlighted = TRUE,
                         label.majority.bases = FALSE, 
                         label.majority.bases.threshold = 0.5, 
                         label.majority.bases.cex = 0.5, 
                         rasterize.plotting.area = FALSE, 
                         raster.height = 1000, 
                         raster.width = 2000,
                         show.base.legend = TRUE, 
                         debugMode, singleEndMode,
                         ...)

Arguments

`plotter`	A `QoRT_Plotter` reference object. See `build.plotter`.
`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

This plot displays the nucleotide rates by read cycle. The color scheme for NVC plots is different from all other plots. Rather than being used for emphasis or to allow cross-comparisons by sample, biological-condition, or lane, the colors are used to indicate the four nucleotides: A (green), T (red), G (orange), or C (blue). Depending on the type of QoRT_Plotter being used, sample-runs will be marked and differentiated by marking the lines with shapes (R points). In many cases the points will be unreadable due to overplotting, but clear outliers that stray from the general trends can be readily identified.

When used with a "sample.highlight" type QoRT_Plotter (see build.plotter), "highlighted" samples will be drawn with a deeper shade of the given color.

makePlot.raw.NVC plots the nucleotides of all cycles of all aligned reads. makePlot.minus.clipping.NVC plots the nucleotides for all cycles that are NOT soft-clipped by the aligner. Note that for reads aligned with an aligner that does not perform soft-clipping (such as TopHat2), the two plots will be identical.

Examples

  data(res,package="QoRTsExampleData");
  plotter <- build.plotter.colorByGroup(res);
  makePlot.minus.clipping.NVC(plotter);

## Starting: NVC, Aligned bases only plot.
## Finished: NVC, Aligned bases only plot.[time: 2016-01-28 16:33:05],[elapsed: 0.75 secs]

plot of chunk unnamed-chunk-1

  makePlot.raw.NVC(plotter);

## Starting: NVC, Raw plot.
## Finished: NVC, Raw plot.[time: 2016-01-28 16:33:06],[elapsed: 0.8 secs]