R: Plot clipped nucleotide rates, aligned by the distance from...

makePlot.NVC.clip.matchByClipPosition {QoRTs}

R Documentation

Plot clipped nucleotide rates, aligned by the distance from the point of clipping.

Description

WARNING: THESE FUNCTIONS ARE BETA, AND ARE NOT FULLY TESTED OR READY FOR GENERAL USE.

Usage

makePlot.NVC.lead.clip.matchByClipPosition(plotter, 
            clip.amt,  r2.buffer, 
            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, 
            load.results = TRUE, 
            debugMode, singleEndMode, 
            plot = TRUE,
            ...)

makePlot.NVC.tail.clip.matchByClipPosition(plotter, 
            clip.amt, r2.buffer,
            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, 
            plot = TRUE,
            ...)

Arguments

`plotter`	A `QoRT_Plotter` reference object. See `build.plotter`.
`clip.amt`	UNDOCUMENTED
`r2.buffer`	UNDOCUMENTED
`label.majority.bases`	UNDOCUMENTED
`label.majority.bases.threshold`	UNDOCUMENTED
`label.majority.bases.cex`	UNDOCUMENTED
`show.base.legend`	UNDOCUMENTED
`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.
`load.results`	UNDOCUMENTED
`debugMode`	UNDOCUMENTED
`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

This function is currently BETA, and is not intended for general use. Documentation and testing is still pending.

Plot clipped nucleotide rates, aligned by the distance from the point of clipping.

Description

Usage

Arguments

Details

See Also