plot.permTestResultsList {regioneR} | R Documentation

## Function for plotting the results from a `permTestResultsList` object when more than one evaluation function was used.

### Description

Function for plotting the results from a `permTestResultsList` object when more than one evaluation function was used.

### Usage

    ## S3 method for class 'permTestResultsList'
    plot(x, ncol = NA, pvalthres = 0.05,
      plotType = "Tailed", main = "", xlab = NULL, ylab = "", ...)

### Arguments

`x` | an object of class `permTestResultsList`.
`ncol` | number of plots per row. ncol=NA means ncol=floor(sqrt(length(x)))so the plot is more or less square (default=NA)
`pvalthres` | p-value threshold for significance. Default is 0.05.
`plotType` | the type of plot to display. This must be one of `"Area"` or `"Tailed"`. Default is `"Area"`.
`main` | a character specifying the title of the plot. Defaults to "".
`xlab` | a character specifying the label of the x axis. Defaults to NULL, which produces a plot with the evaluation function name as the x axis label.
`ylab` | a character specifying the label of the y axis. Defaults to "".
`...` | further arguments to be passed to or from methods.

### Value

A plot is created on the current graphics device.

### See Also

`permTest`

### Examples

    genome <- filterChromosomes(getGenome("hg19"), keep.chr="chr1")
    A <- createRandomRegions(nregions=20, length.mean=10000000, length.sd=20000, genome=genome, non.overlapping=FALSE)
    B <- c(A, createRandomRegions(nregions=10, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE))

    pt <- overlapPermTest(A=A, B=B, ntimes=10, genome=genome, non.overlapping=FALSE)
    summary(pt)
    plot(pt)
    plot(pt, plotType="Tailed")

    pt2 <- permTest(A=A, B=B, ntimes=10, alternative="auto", genome=genome, evaluate.function=list(distance=meanDistance, numberOfOverlaps=numOverlaps), randomize.function=randomizeRegions, non.overlapping=FALSE)
    summary(pt2)
    plot(pt2)
    plot(pt2, plotType="Tailed")

[Package regioneR version 1.20.1 Index]