SEXP hclustCombinedMatrix(SEXP mpcrossRF_, SEXP preClusterResults_)
{
BEGIN_RCPP
bool noDuplicates;
R_xlen_t preClusterMarkers = countPreClusterMarkers(preClusterResults_, noDuplicates);
if(!noDuplicates)
{
throw std::runtime_error("Duplicate marker indices in call to hclustThetaMatrix");
}
Rcpp::List preClusterResults = preClusterResults_;
Rcpp::S4 mpcrossRF = mpcrossRF_;
Rcpp::S4 rf = mpcrossRF.slot("rf");
Rcpp::RObject lodObject = rf.slot("lod");
if(lodObject.isNULL())
{
throw std::runtime_error("Slot mpcrossRF@rf@lod cannot be NULL if clusterBy is equal to \"combined\"");
}
Rcpp::S4 lod = Rcpp::as<Rcpp::S4>(lodObject);
Rcpp::S4 theta = rf.slot("theta");
Rcpp::RawVector data = theta.slot("data");
Rcpp::NumericVector levels = theta.slot("levels");
Rcpp::CharacterVector markers = theta.slot("markers");
Rcpp::NumericVector lodData = lod.slot("x");
if(markers.size() != preClusterMarkers || lodData.size() != (preClusterMarkers*(preClusterMarkers+(R_xlen_t)1))/(R_xlen_t)2)
{
throw std::runtime_error("Number of markers in precluster object was inconsistent with number of markers in mpcrossRF object");
}
R_xlen_t resultDimension = preClusterResults.size();
//Work out minimum difference between recombination levels
double minDifference = 1;
for(int i = 0; i < levels.size()-1; i++)
{
minDifference = std::min(minDifference, levels[i+1] - levels[i]);
}
double maxLod = *std::max_element(lodData.begin(), lodData.end());
double lodMultiplier = minDifference/maxLod;
//Allocate enough storage. This symmetric matrix stores the *LOWER* triangular part, in column-major storage. Excluding the diagonal.
Rcpp::NumericVector result(((resultDimension-(R_xlen_t)1)*resultDimension)/(R_xlen_t)2);
for(R_xlen_t column = 0; column < resultDimension; column++)
{
Rcpp::IntegerVector columnMarkers = preClusterResults(column);
for(R_xlen_t row = column + (R_xlen_t)1; row < resultDimension; row++)
{
Rcpp::IntegerVector rowMarkers = preClusterResults(row);
double total = 0;
R_xlen_t counter = 0;
for(int columnMarkerCounter = 0; columnMarkerCounter < columnMarkers.size(); columnMarkerCounter++)
{
R_xlen_t marker1 = columnMarkers[columnMarkerCounter]-(R_xlen_t)1;
for(int rowMarkerCounter = 0; rowMarkerCounter < rowMarkers.size(); rowMarkerCounter++)
{
R_xlen_t marker2 = rowMarkers[rowMarkerCounter]-(R_xlen_t)1;
R_xlen_t column = std::max(marker1, marker2);
R_xlen_t row = std::min(marker1, marker2);
Rbyte thetaDataValue = data((column*(column+(R_xlen_t)1))/(R_xlen_t)2 + row);
double currentLodDataValue = lodData((column*(column+(R_xlen_t)1))/(R_xlen_t)2 + row);
if(thetaDataValue != 0xFF && currentLodDataValue != NA_REAL && currentLodDataValue == currentLodDataValue)
{
total += levels(thetaDataValue) + (maxLod - currentLodDataValue) *lodMultiplier;
counter++;
}
}
}
if(counter == 0) total = 0.5 + minDifference;
else total /= counter;
result(((resultDimension-1)*resultDimension)/(R_xlen_t)2 - ((resultDimension - column)*(resultDimension-column-(R_xlen_t)1))/(R_xlen_t)2 + row-column-(R_xlen_t)1) = total;
}
}
return result;
END_RCPP
}
SEXP hclustLodMatrix(SEXP mpcrossRF_, SEXP preClusterResults_)
{
BEGIN_RCPP
bool noDuplicates;
R_xlen_t preClusterMarkers = countPreClusterMarkers(preClusterResults_, noDuplicates);
if(!noDuplicates)
{
throw std::runtime_error("Duplicate marker indices in call to hclustThetaMatrix");
}
Rcpp::List preClusterResults = preClusterResults_;
Rcpp::S4 mpcrossRF = mpcrossRF_;
Rcpp::S4 rf = mpcrossRF.slot("rf");
Rcpp::RObject lodObject = rf.slot("lod");
if(lodObject.isNULL())
{
throw std::runtime_error("Slot mpcrossRF@rf@lod cannot be NULL if clusterBy is equal to \"combined\"");
}
Rcpp::S4 lod = Rcpp::as<Rcpp::S4>(lodObject);
Rcpp::NumericVector lodData = lod.slot("x");
if(lodData.size() != (preClusterMarkers*(preClusterMarkers+(R_xlen_t)1))/(R_xlen_t)2)
{
throw std::runtime_error("Number of markers in precluster object was inconsistent with number of markers in mpcrossRF object");
}
R_xlen_t resultDimension = preClusterResults.size();
double maxLod = *std::max_element(lodData.begin(), lodData.end());
//Allocate enough storage. This symmetric matrix stores the *LOWER* triangular part, in column-major storage. Excluding the diagonal.
Rcpp::NumericVector result(((resultDimension-(R_xlen_t)1)*resultDimension)/(R_xlen_t)2);
for(R_xlen_t column = 0; column < resultDimension; column++)
{
Rcpp::IntegerVector columnMarkers = preClusterResults(column);
for(R_xlen_t row = column + 1; row < resultDimension; row++)
{
Rcpp::IntegerVector rowMarkers = preClusterResults(row);
double total = 0;
int counter = 0;
for(R_xlen_t columnMarkerCounter = 0; columnMarkerCounter < columnMarkers.size(); columnMarkerCounter++)
{
R_xlen_t marker1 = columnMarkers[columnMarkerCounter]-(R_xlen_t)1;
for(R_xlen_t rowMarkerCounter = 0; rowMarkerCounter < rowMarkers.size(); rowMarkerCounter++)
{
R_xlen_t marker2 = rowMarkers[rowMarkerCounter]-(R_xlen_t)1;
R_xlen_t column = std::max(marker1, marker2);
R_xlen_t row = std::min(marker1, marker2);
double currentLodDataValue = lodData((column*(column+(R_xlen_t)1))/(R_xlen_t)2 + row);
if(currentLodDataValue != NA_REAL && currentLodDataValue == currentLodDataValue)
{
total += currentLodDataValue;
counter++;
}
}
}
if(counter == 0) total = maxLod;
else total /= counter;
result(((resultDimension-(R_xlen_t)1)*resultDimension)/(R_xlen_t)2 - ((resultDimension - column)*(resultDimension-column-(R_xlen_t)1))/(R_xlen_t)2 + row-column-(R_xlen_t)1) = maxLod - total;
}
}
return result;
END_RCPP;
}