plot.permTestResults {regioneR} | R Documentation |
permTestResults
object.Function for plotting the results from a permTestResults
object.
## S3 method for class 'permTestResults' plot(x, pvalthres = 0.05, plotType = "Tailed", main = "", xlab = NULL, ylab = "", ylim = NULL, xlim = NULL, ...)
x |
an object of class |
pvalthres |
p-value threshold for significance. Default is 0.05. |
plotType |
the type of plot to display. This must be one of |
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 "". |
ylim |
defines the y limits of the plot. Passed to the underlying |
xlim |
defines the x limits of the plot. Passed to the underlying |
... |
further arguments to be passed to or from methods. |
A plot is created on the current graphics device.
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=meanDistance, randomize.function=randomizeRegions, non.overlapping=FALSE) summary(pt2) plot(pt2) plot(pt2, plotType="Tailed")