plotRle: Plotting functions for Rle objects
In jotsetung/GenomePlotR: Plotting data in genomic context

Description Usage Arguments Details Value Functions Author(s) See Also

View source: R/plotRle.R

These functions provide some functionality to visualize (numeric) Rle (run length encoded) objects.

  ## S4 method for signature 'Rle'
boxplot( x, range=1.5, ... )

  ## S4 method for signature 'Rle'
plot( x, y, ... )

  plotRle( x, add=FALSE, offset=0, ylab="values", xlab="position", ... )

  rleboxplot( x, range=1.5, ... )

  rleboxplot.stats( x, coef=1.5, do.conf=TRUE, do.out=FALSE )

`add`	Whether the data should be added to an existing plot.
`coef`	see help for function `boxplot.stats` for details.
`do.conf`	whether confidence intervals should be calculated. See help for function `boxplot.stats` for more details.
`do.out`	whether outliers should be returned; see help for function `boxplot.stats` for more details. Setting this to `TRUE` for a large `Rle` object is discouraged.
`offset`	amount by which the x-position values should be shifted.
`range`	see help for function `boxplot` for details.
`x`	A `Rle` object.
`xlab`	the label for the x-axis.
`y`	Not used.
`ylab`	the label for the y-axis.
`...`	Additional arguments to be passed to the `plot` or `points` function (like `pch` for point type, `col` for the color).

These functions allows to efficiently plot a run-length encoded object.

A plot.

boxplot: creates a boxplot for a Rle object.
plot: plots a Rle object; this function calls plotRle.
plotRle: plots a (numeric!) Rle object. This function is much more efficient than the standard plot function on Rle objects as, instead of plotting each individual value, it plots just the changes (i.e. the runs).
rleboxplot: creates a boxplot for a Rle object; uses the rleboxplot.stats function to calculate the required values and the bxp for the actual plotting.
rleboxplot.stats: calculates the required statistics to generate a boxplot; works on both, numeric Rle objects or numeric vectors.