plot.permTestResultsList {regioneR} | R Documentation |
permTestResultsList
object when more than one evaluation function was used.Function for plotting the results from a permTestResultsList
object when more than one evaluation function was used.
## S3 method for class 'permTestResultsList' plot(x, ncol = NA, pvalthres = 0.05, plotType = "Tailed", main = "", xlab = NULL, ylab = "", ...)
x |
an object of class |
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 |
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. |
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=list(distance=meanDistance, numberOfOverlaps=numOverlaps), randomize.function=randomizeRegions, non.overlapping=FALSE) summary(pt2) plot(pt2) plot(pt2, plotType="Tailed")