plotsnpfreq: Plot frequency of polymorphic sites

In seedy: Simulation of Evolutionary and Epidemiological Dynamics

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.

Details

Plots frequency of polymorphic sites above each probability level.

Value

Returns a matrix with points used for the plot.

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)

seedy documentation built on May 29, 2017, 10:58 a.m.