plot.allele.freq: Plots population allele frequencies per locus represented by...

In UWMAlberto-Lab/StandArich2: Standardizes n to estimate allelic richness and plots

Plots population allele frequencies per locus represented by dots of varying size

Description

For each locus a plot is constructed in a new window. Allele frequencies are represented by dots of varying diameter. Allele codes are indicated on the x axis and populations on the y axis

Usage

plot.allele.freq(data, LocusNames,Plogbase=20,textlegend=0.8,freqlegend=c(0.1,0.15,0.2,0.5,0.75,1),
                psize=7,poptext=0.5,allelesize=1,xaxispos=0,yplotlim=-3,alleleangle=45,
                pdfout=FALSE,pdfname="out.pdf")

Arguments

data	A data.frame with rows corresponding to individuals and populations on top of each other. The first column has the population codes, the 2nd the individual codes. The following columns have the allele codes, in integers, using three or two digits (but be consistent!). Missing data is represented by the value 999. There is no header in this file
LocusNames	a character vector with the names of loci
Plogbase	used to control the points cex argument to plot allele frequencies as points, as in cex=log(allelefreq+1,base=Plogbase)*psize)
textlegend	controls the cex argument for the legend text size
freqlegend	a numeric vector with the allele frequencies used in the legend
poptext	controls the cex argument for the font size of population names in the y-axis. Defaults to 0.5
pcol	color of points for each population takes a vector of with length equal to the number of populations. Defaults to black
allelesize	controls the cex argument for the font size of allele names in the x-axis
xaxispos	the pos argument for horizontal axis in the plot, see help(axis)
yplotlim	The ylim argument of the plot, see help(plot.default)
alleleangle	text rotation for allele names, in degrees, defaults to 45
pdfout	logical to control if a pdf with the plot should be written, defaults to FALSE. Currently the function to export pdf is not working in RStudio
psize	Used to control the points cex argument to plot allele frequencies as points, as in cex=log(allelefreq+1,base=Plogbase)*psize
pdfname	Name for the output pdf file to write the plots if pdfout is TRUE, defaults to out.pdf

Details

Depending on the number of populations and alleles in the data set, different combinations of psize and Plogbase arguments should be tried

Value

As many different plot windows as there are loci in the data file, allowing a visualization of allele frequencies at each locus across populations

Author(s)

Filipe Alberto, Department of Biological Sciences, University of Wisconsin-Milwaukee

References

Alberto F, Arnaud-Haond S, Duarte CM, Serrao EA (in press) Genetic diversity of a clonal angiosperm near its range limit: the case of Cymodocea nodosa in the Canary Islands. Marine Ecology Progress Series

See Also

plot.allele.freq, allele.genotype.plot

Examples

data(Exdata)
allele.freq.plot(Exdata,LocusNames=paste("L",1:8,sep="."))

{ dplot }

UWMAlberto-Lab/StandArich2 documentation built on March 28, 2023, 1:10 a.m.