Site frequency spectrum plot

Plots the site frequency spectrum.

# S3 method for DNAmat_class
plot(DNAmat, xlab = "Index i",
  ylab = "Number of i-tons", main = "Site frequency spectrum", ...)

Arguments

DNAmat	matrix; either a single-nucleotide polymorphism matrix or a segregating sites matrix of class 'DNAmat_class'. See SNP for explanation.
xlab	a title for the x axis. Is by default "Index i". See title.
ylab	a title for the y axis. Is by default "Number of i-tons". See title.
main	an overall title for the plot. Is by default "Site frequency spectrum". See title.
...	arguments passed on from plot.

Details

The terminology "Number of i-tons" corresponds to the i'th entry in the site frequency spectrum. See SFS for further explanation.

Examples

# Using the function simDNAseq:
plot(simDNAseq(n = 8, seqLen = 20, mutRate = 5,
               popType = "varPop", expRate = 1.5), col="red")


# Creating a segregating sites matrix by hand:
SegSitesMat <- matrix(sample(x=c(0, 1), size=26*12,
                      replace=TRUE, prob=c(0.9, 0.1)),
                      nrow=12, ncol=26, byrow=TRUE)
class(SegSitesMat) <- "DNAmat_class"
plot(SegSitesMat)