# Plots a heat map depicting the probability an unknown individual comes from each block

### Description

This function plots a probability heat map surface outputted by FitOriGenModelFindUnknowns.

### Usage

1 | ```
PlotUnknownHeatMap(HeatMapOutput,UnknownNumber=1,MaskWater=TRUE)
``` |

### Arguments

`HeatMapOutput` |
The output of |

`UnknownNumber` |
Integer indicating the unknown individual heat map number to plot. |

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

### Value

This outputs a plot of the probability heat map for a particular unknown individual.

### Author(s)

John Michael Ranola, John Novembre, and Kenneth Lange

### References

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

### See Also

`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`

,

### Examples

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | ```
#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)
## End(Not run)
``` |