seedy (version 1.3)

plotsnpfreq: Plot frequency of polymorphic sites

Description

Returns the frequency of polymorphic sites above a probability level.

Usage

plotsnpfreq(data, timepoint=1, type="S", ...)

Arguments

data

Full sequence data generated from the simulatepopulation function.

timepoint

Which sampling time should be used.

type

Type of plot desired. See plot.

...

Additional arguments to be passed to plot.

Value

• Returns a matrix with points used for the plot.

Details

Plots frequency of polymorphic sites above each probability level.

Examples

data(deepseq)

# At the 25th time point
plotsnpfreq(data=deepseq, timepoint=25, xlab="Mutant frequency", ylim=c(0,25),
      ylab="No. sites", yaxs="i", xaxs="i", las=1, bty="l", col="red", lwd=2)
# At the 50th time point
plotsnpfreq(data=deepseq, timepoint=50, xlab="Mutant frequency", ylim=c(0,25),
      ylab="No. sites", yaxs="i", xaxs="i", las=1, bty="l", col="red", lwd=2)