// [[Rcpp::export]]
Rcpp::IntegerMatrix quantileNorm(Rcpp::IntegerMatrix mat, Rcpp::IntegerVector ref, int nthreads=1, int seed=13){
if (mat.nrow() != ref.length()) Rcpp::stop("incompatible arrays...");
if (!std::is_sorted(ref.begin(), ref.end())) Rcpp::stop("ref must be sorted");
int ncol = mat.ncol();
int nrow = mat.nrow();
//allocate new matrix
Rcpp::IntegerMatrix res(nrow, ncol);
Mat<int> oldmat = asMat(mat);
Mat<int> newmat = asMat(res);
Vec<int> ref2 = asVec(ref);
//allocate a seed for each column
std::seed_seq sseq{seed};
std::vector<std::uint32_t> seeds(ncol);
sseq.generate(seeds.begin(), seeds.end());
#pragma omp parallel num_threads(nthreads)
{
std::vector<std::pair<int, int> > storage(nrow);//pairs <value, index>
#pragma omp for
for (int col = 0; col < ncol; ++col){
std::mt19937 gen(seeds[col]);
qtlnorm(oldmat.getCol(col), ref2, newmat.getCol(col), storage, gen);
}
}
res.attr("dimnames") = mat.attr("dimnames");
return res;
}
void CEnv::SetData(Rcpp::IntegerMatrix x_, Rcpp::IntegerMatrix mcz_) {
int J = x_.nrow();
int n = x_.ncol();
int nZeroMC = mcz_.ncol();
if (mcz_.nrow() != J) { // no mcz
nZeroMC = 0;
}
intvec x = Rcpp::as<intvec>(x_);
intvec mcz = Rcpp::as<intvec>(mcz_);
Rcpp::List something(x_.attr("levels"));
intvec levels(something.size());
for (unsigned int i = 0; i < levels.size(); i++) {
SEXP exp = something[i];
Rcpp::CharacterVector v(exp);
levels[i] = v.size();
//Rprintf( "%d\n", levels[i]) ;
}
SetData(x, J, n, mcz, nZeroMC, levels);
}
// [[Rcpp::export]]
Rcpp::NumericMatrix CramersV_DF(Rcpp::IntegerMatrix dm, bool Bias_Cor) {
int iCol = dm.ncol();
int i=0,j=0;
Rcpp::NumericMatrix ResCV(iCol,iCol);
for (i=0;i<iCol;i++){
for (j=i;j<iCol;j++){
if(i==j) {ResCV(i,j)=1;}
else {
ResCV(i,j) = CramersV_C((IntegerVector)dm(_,i),(IntegerVector)dm(_,j),(bool)Bias_Cor);
ResCV(j,i) = ResCV(i,j);
}
}
}
Rcpp::List dimnms = Rcpp::List::create(VECTOR_ELT(dm.attr("dimnames"), 1),
VECTOR_ELT(dm.attr("dimnames"), 1));
ResCV.attr("dimnames")=dimnms;
return ResCV;
}
/* This function specifically checks whether the observed data is consistent with the *pedigree*. It assumes that every observed value in the finals is already valid - That is, every observed value contained in the finals is also listed as a possibility in the hetData object
*/
void estimateRFCheckFunnels(Rcpp::IntegerMatrix finals, Rcpp::IntegerMatrix founders, Rcpp::List hetData, Rcpp::S4 pedigree, std::vector<int>& intercrossingGenerations, std::vector<std::string>& warnings, std::vector<std::string>& errors, std::vector<funnelType>& allFunnels, std::vector<funnelType>& lineFunnels)
{
Rcpp::CharacterVector pedigreeLineNames = Rcpp::as<Rcpp::CharacterVector>(pedigree.slot("lineNames"));
//We make a copy of the pedigree line names and sort it (otherwise the std::find relating to pedigreeLineNames is prohibitive)
std::vector<pedigreeLineStruct> sortedLineNames;
sortPedigreeLineNames(pedigreeLineNames, sortedLineNames);
Rcpp::IntegerVector mother = Rcpp::as<Rcpp::IntegerVector>(pedigree.slot("mother"));
Rcpp::IntegerVector father = Rcpp::as<Rcpp::IntegerVector>(pedigree.slot("father"));
bool warnImproperFunnels = Rcpp::as<bool>(pedigree.slot("warnImproperFunnels"));
Rcpp::CharacterVector finalNames = Rcpp::as<Rcpp::CharacterVector>(Rcpp::as<Rcpp::List>(finals.attr("dimnames"))[0]);
Rcpp::CharacterVector markerNames = Rcpp::as<Rcpp::CharacterVector>(Rcpp::as<Rcpp::List>(finals.attr("dimnames"))[1]);
int nFinals = finals.nrow(), nFounders = founders.nrow(), nMarkers = finals.ncol();
if(nFounders != 2 && nFounders != 4 && nFounders != 8 && nFounders != 16)
{
throw std::runtime_error("Number of founders must be 2, 4, 8, or 16");
}
xMajorMatrix<int> foundersToMarkerAlleles(nFounders, nFounders, nMarkers, -1);
for(int markerCounter = 0; markerCounter < nMarkers; markerCounter++)
{
Rcpp::IntegerMatrix currentMarkerHetData = hetData(markerCounter);
for(int founderCounter1 = 0; founderCounter1 < nFounders; founderCounter1++)
{
for(int founderCounter2 = 0; founderCounter2 < nFounders; founderCounter2++)
{
int markerAllele1 = founders(founderCounter1, markerCounter);
int markerAllele2 = founders(founderCounter2, markerCounter);
for(int hetDataRowCounter = 0; hetDataRowCounter < currentMarkerHetData.nrow(); hetDataRowCounter++)
{
if(markerAllele1 == currentMarkerHetData(hetDataRowCounter, 0) && markerAllele2 == currentMarkerHetData(hetDataRowCounter, 1))
{
foundersToMarkerAlleles(founderCounter1, founderCounter2, markerCounter) = currentMarkerHetData(hetDataRowCounter, 2);
}
}
}
}
}
std::vector<long> individualsToCheckFunnels;
for(long finalCounter = 0; finalCounter < nFinals; finalCounter++)
{
individualsToCheckFunnels.clear();
std::string currentLineName = Rcpp::as<std::string>(finalNames(finalCounter));
std::vector<pedigreeLineStruct>::iterator findLineName = std::lower_bound(sortedLineNames.begin(), sortedLineNames.end(), pedigreeLineStruct(currentLineName, -1));
if(findLineName == sortedLineNames.end() || findLineName->lineName != currentLineName)
{
std::stringstream ss;
ss << "Unable to find line number " << finalCounter << " named " << finalNames(finalCounter) << " in pedigree";
throw std::runtime_error(ss.str().c_str());
}
int pedigreeRow = findLineName->index;
//This vector lists all the founders that are ancestors of the current line. This may comprise any number - E.g. if we have an AIC line descended from funnels 1,2,1,2 and 2,3,2,3 then this vector is going it contain 1,2,3
std::vector<int> representedFounders;
if(intercrossingGenerations[finalCounter] == 0)
{
individualsToCheckFunnels.push_back(pedigreeRow);
}
else
{
try
{
getAICParentLines(mother, father, pedigreeRow, intercrossingGenerations[finalCounter], individualsToCheckFunnels);
}
catch(...)
{
std::stringstream ss;
ss << "Error while attempting to trace intercrossing lines for line " << finalNames(finalCounter);
errors.push_back(ss.str());
goto nextLine;
}
}
//Now we know the lines for which we need to check the funnels from the pedigree (note: We don't necessarily have genotype data for all of these, it's purely a pedigree check)
//Fixed length arrays to store funnels. If we have less than 16 founders then part of this is garbage and we don't use that bit....
funnelType funnel, copiedFunnel;
for(std::vector<long>::iterator i = individualsToCheckFunnels.begin(); i != individualsToCheckFunnels.end(); i++)
{
try
{
getFunnel(*i, mother, father, &(funnel.val[0]), nFounders);
}
catch(...)
{
std::stringstream ss;
ss << "Attempting to trace pedigree for line " << finalNames(finalCounter) << ": Unable to get funnel for line " << pedigreeLineNames(*i);
errors.push_back(ss.str());
goto nextLine;
}
//insert these founders into the vector containing all the represented founders
representedFounders.insert(representedFounders.end(), &(funnel.val[0]), &(funnel.val[0]) + nFounders);
//Copy the funnel
memcpy(&copiedFunnel, &funnel, sizeof(funnelType));
std::sort(&(copiedFunnel.val[0]), &(copiedFunnel.val[0]) + nFounders);
if(std::unique(&(copiedFunnel.val[0]), &(copiedFunnel.val[0]) + nFounders) != &(copiedFunnel.val[0]) + nFounders)
{
//If we have intercrossing generations then having repeated founders is an error. Otherwise if warnImproperFunnels is true it's still a warning.
if(intercrossingGenerations[finalCounter] != 0 || warnImproperFunnels)
{
std::stringstream ss;
ss << "Funnel for line " << pedigreeLineNames(*i) << " contained founders {" << funnel.val[0];
if(nFounders == 2)
{
ss << ", " << funnel.val[1] << "}";
}
else if(nFounders == 4)
{
ss << ", " << funnel.val[1] << ", " << funnel.val[2] << ", " << funnel.val[3] << "}";
}
else if(nFounders == 8)
{
ss << ", " << funnel.val[1] << ", " << funnel.val[2] << ", " << funnel.val[3] << ", " << funnel.val[4] << ", " << funnel.val[5] << ", " << funnel.val[6] << ", " << funnel.val[7]<< "}";
}
else if (nFounders == 16)
{
ss << ", " << funnel.val[1] << ", " << funnel.val[2] << ", " << funnel.val[3] << ", " << funnel.val[4] << ", " << funnel.val[5] << ", " << funnel.val[6] << ", " << funnel.val[7] << ", " << funnel.val[8] << ", " << funnel.val[9] << ", " << funnel.val[10] << ", " << funnel.val[11] << ", " << funnel.val[12] << ", " << funnel.val[13] << ", " << funnel.val[14] << ", " << funnel.val[15] << "}";
}
//In this case it's an error
if(intercrossingGenerations[finalCounter] != 0)
{
ss << ". Repeated founders are only allowed with zero generations of intercrossing";
errors.push_back(ss.str());
}
//But if we have zero intercrossing generations then it's only a warning
else
{
ss << ". Did you intend to use all " << nFounders << " founders?";
warnings.push_back(ss.str());
}
}
}
allFunnels.push_back(funnel);
}
//remove duplicates in representedFounders
std::sort(representedFounders.begin(), representedFounders.end());
representedFounders.erase(std::unique(representedFounders.begin(), representedFounders.end()), representedFounders.end());
//Try and check for inconsistent generations of selfing
for(std::vector<int>::iterator i = representedFounders.begin(); i != representedFounders.end(); i++)
{
if(*i > nFounders)
{
std::stringstream ss;
ss << "Error in pedigree for line number " << finalCounter << " named " << finalNames(finalCounter) << ". Inconsistent number of generations of intercrossing";
errors.push_back(ss.str());
goto nextLine;
}
}
//Not having all the founders in the input funnels is more serious if it causes the observed marker data to be impossible. So check for this.
for(int markerCounter = 0; markerCounter < nMarkers; markerCounter++)
{
bool okMarker = false;
//If observed value is an NA then than's ok, continue
int value = finals(finalCounter, markerCounter);
if(value == NA_INTEGER) continue;
for(std::vector<int>::iterator founderIterator1 = representedFounders.begin(); founderIterator1 != representedFounders.end(); founderIterator1++)
{
for(std::vector<int>::iterator founderIterator2 = representedFounders.begin(); founderIterator2 != representedFounders.end(); founderIterator2++)
{
//Note that founderIterator comes from representedFounders, which comes from getFunnel - Which returns values starting at 1, not 0. So we have to subtract one.
if(finals(finalCounter, markerCounter) == foundersToMarkerAlleles((*founderIterator1)-1, (*founderIterator2)-1, markerCounter))
{
okMarker = true;
break;
}
}
}
if(!okMarker)
{
std::stringstream ss;
ss << "Data for marker " << markerNames(markerCounter) << " is impossible for individual " << finalNames(finalCounter) << " with given pedigree";
errors.push_back(ss.str());
if(errors.size() > 1000) return;
goto nextLine;
}
}
//In this case individualsToCheckFunnels contains one element => getFunnel was only called once => we can reuse the funnel variable
if(intercrossingGenerations[finalCounter] == 0)
{
orderFunnel(&(funnel.val[0]), nFounders);
lineFunnels.push_back(funnel);
}
else
{
//Add a dummy value in lineFunnel
for(int i = 0; i < 16; i++) funnel.val[i] = 0;
lineFunnels.push_back(funnel);
}
nextLine:
;
}
}
// [[Rcpp::export]]
XPtrImage magick_image_readbitmap_native(Rcpp::IntegerMatrix x){
Rcpp::IntegerVector dims(x.attr("dim"));
return magick_image_bitmap(x.begin(), Magick::CharPixel, 4, dims[1], dims[0]);
}