seedy (version 1.3)

plotdiversity: Plot genetic diversity over time

Description

Calculates and plots the genetic diversity (mean pairwise number of SNPs between samples) in deep-sequenced samples.

Usage

plotdiversity(X, sample.times, makeplot = TRUE, filter=FALSE, ...)

Arguments

X

Simulated deep sequence data over time.

sample.times

Vector of sample collection times.

makeplot

Should diversity samples be plotted?

filter

Should a subset of the sequence data be plotted? That is, should only the sequences at sample.times be plotted, out of a larger sample set?

...

Additional arguments to be passed to plot (if makeplot=TRUE).

Value

• Returns a vector of diversity values for each sample time.

Examples

data(deepseq)
D <- plotdiversity(deepseq, sample.times=(1:50)*1000, xlab="Time", 
                   ylab="Expected pairwise SNPs")