PlotUnknownHeatMap {OriGen} | R Documentation |
This function plots a probability heat map surface outputted by FitOriGenModelFindUnknowns.
PlotUnknownHeatMap(HeatMapOutput,UnknownNumber=1,MaskWater=TRUE)
HeatMapOutput |
The output of |
UnknownNumber |
Integer indicating the unknown individual heat map number to plot, "ALL" which would plot best locations for all samples, or "GROUP" which plots a heat map assuming the entire group came from a single location. |
MaskWater |
Logical value that if true removes water from the plotted regions. |
This outputs a plot of the probability heat map for a particular unknown individual.
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.
ConvertUnknownPEDData
for converting two Plink PED files (known and unknown)into a format appropriate for analysis,
FitOriGenModelFindUnknowns
for fitting allele surfaces to the converted data and finding the locations of the given unknown individuals,
PlotUnknownHeatMap
for a quick way to plot the resulting unknown heat map surfaces from FitOriGenModelFindUnknowns
,
FitAdmixedModelFindUnknowns
for fitting allele surfaces to the converted data and finding the locations of the given unknown individuals who may be admixed,
PlotAdmixedSurface
for a quick way to plot the resulting admixture surfaces from FitAdmixedFindUnknowns
,
#this example not run because it takes slightly 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 NumberSNPs=5 TestData=array(sample(2*(1:30),2*SampleSites*NumberSNPs,replace=TRUE), dim=c(2,SampleSites,NumberSNPs)) #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) #This code simulates the number of major alleles the unknown individuals have. NumberUnknowns=2 TestUnknowns=array(sample(0:2,NumberUnknowns*NumberSNPs,replace=TRUE), dim=c(NumberUnknowns,NumberSNPs)) #Fitting the model #MaxGridLength is the maximum number of boxes allowed to span the region in either direction #RhoParameter is a tuning constant trials4=FitOriGenModelFindUnknowns(TestData,TestCoordinates,TestUnknowns, MaxGridLength=20,RhoParameter=10) str(trials4) #Plotting the unknown heat map PlotUnknownHeatMap(trials4,UnknownNumber=1,MaskWater=TRUE) # PlotUnknownHeatMap(trials4,UnknownNumber="ALL",MaskWater=TRUE) # PlotUnknownHeatMap(trials4,UnknownNumber="GROUP",MaskWater=TRUE) ## End(Not run)