OriGen (version 1.4.3)

PlotAlleleFrequencySurface: Plots an OriGen fitted allele frequency surface

Description

This function plots an allele frequency surface outputted by FitOriGenModel and FitMultinomialModel.

Usage

PlotAlleleFrequencySurface(AlleleSurfaceOutput,LocusNumber=1,
		AlleleNumber=1,MaskWater=TRUE,Scale=FALSE)

Arguments

AlleleSurfaceOutput

The output of FitOriGenModel or FitMultinomialModel

LocusNumber

Integer indicating the Locus number to plot.

AlleleNumber

Integer indicating which allele to plot. If using microsatellites and AlleleNumber = 0, then this plots all the allele frequency surfaces in a grid.

MaskWater

Logical value that if true removes water from the plotted regions.

Scale

Logical value that if TRUE will scale the colors to (0,max(Frequency)) instead of (0,1).

Value

• This outputs a plot (using ggplot) of the allele frequency surface on a map.

References

Ranola J, Novembre J, Lange K (2014) Fast Spatial Ancestry via Flexible Allele Frequency Surfaces. Bioinformatics, in press.

See Also

ConvertMicrosatData for converting Microsatellite data files into a format appropriate for analysis, ConvertPEDData for converting Plink PED files into a format appropriate for analysis,

FitOriGenModel for fitting allele surfaces to the converted SNP data,

FitMultinomialModel for fitting allele surfaces to the converted Microsatellite data,

PlotAlleleFrequencySurface for a quick way to plot the resulting allele frequency surfaces from FitOriGenModel or FitMultinomialModel,;

Examples

#this example not run because it takes a little longer than 5 secs
#note - type example(FunctionName, run.dontrun=TRUE) to run the example where FunctionName is
#the name of the function
#Data generation
	SampleSites=10
	NumberLoci=4
	MaxAlleles=4
	NumberAllelesAtEachLocus=sample(2:MaxAlleles,NumberLoci,replace=TRUE)

	TestData=array(0,dim=c(MaxAlleles,SampleSites,NumberLoci))
	for(i in 1:NumberLoci){
		for(j in 1:NumberAllelesAtEachLocus[i]){
			TestData[j,,i]=sample(1:10,SampleSites,replace=TRUE)
		}
	}
	#Europe is about -9 to 38 and 34 to 60
	TestCoordinates=array(0,dim=c(SampleSites,2))
	TestCoordinates[,1]=runif(SampleSites,-9,38)
	TestCoordinates[,2]=runif(SampleSites,34,60)

	#Fitting the model
	#MaxGridLength is the maximum number of boxes allowed to span the region in either direction
	#RhoParameter is a tuning constant
	trials2=FitMultinomialModel(TestData,TestCoordinates,MaxGridLength=20,RhoParameter=10)
	str(trials2)

	#Plotting the model
	PlotAlleleFrequencySurface(trials2)