PlotAlleleFrequencySurface {OriGen} | R Documentation |
This function plots an allele frequency surface outputted by FitOriGenModel and FitMultinomialModel.
PlotAlleleFrequencySurface(AlleleSurfaceOutput,LocusNumber=1, AlleleNumber=1,MaskWater=TRUE,Scale=FALSE)
AlleleSurfaceOutput |
The output of |
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). |
This outputs a plot (using ggplot) of the allele frequency surface on a map.
John Michael Ranola, John Novembre, and Kenneth Lange
Ranola J, Novembre J, Lange K (2014) Fast Spatial Ancestry via Flexible Allele Frequency Surfaces. Bioinformatics, in press.
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
,;
#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 ## Not run: #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) ## End(Not run)