Rcpp_exports.cpp

#include <RcppArmadillo.h>
#include <RcppEigen.h>
#include <progress.hpp>
#include <cmath>
#include <unordered_map>
#include <fstream>
#include <string>

using namespace Rcpp;
// [[Rcpp::depends(RcppArmadillo)]]
// [[Rcpp::depends(RcppEigen)]]
// [[Rcpp::depends(RcppProgress)]]


// [[Rcpp::export]]
SEXP armaMatMult(arma::mat A, arma::mat B){
  arma::mat C = A * B;
  
  return Rcpp::wrap(C);
}

// [[Rcpp::export]]
SEXP eigenMatMult(Eigen::MatrixXd A, Eigen::MatrixXd B){
  Eigen::MatrixXd C = A * B;
  
  return Rcpp::wrap(C);
}

// [[Rcpp::export]]
SEXP eigenMapMatMult(const Eigen::Map<Eigen::MatrixXd> A, Eigen::Map<Eigen::MatrixXd> B){
  Eigen::MatrixXd C = A * B;
  
  return Rcpp::wrap(C);
}

// [[Rcpp::export]]
NumericMatrix fastPdist2(NumericMatrix Ar, NumericMatrix Br) {
  int m = Ar.nrow(), 
    n = Br.nrow(),
    k = Ar.ncol();
  arma::mat A = arma::mat(Ar.begin(), m, k, false); 
  arma::mat B = arma::mat(Br.begin(), n, k, false); 
  
  arma::colvec An =  sum(square(A),1);
  arma::colvec Bn =  sum(square(B),1);
  
  arma::mat C = -2 * (A * B.t());
  C.each_col() += An;
  C.each_row() += Bn.t();
  
  return wrap(sqrt(C)); 
}

// [[Rcpp::export]]
Eigen::SparseMatrix<double> LogNorm(Eigen::SparseMatrix<double> data, int scale_factor, bool display_progress = true){
  Progress p(data.outerSize(), display_progress);
  Eigen::VectorXd colSums = data.transpose() * Eigen::VectorXd::Ones(data.rows());
  for (int k=0; k < data.outerSize(); ++k){
    p.increment();
    for (Eigen::SparseMatrix<double>::InnerIterator it(data, k); it; ++it){
      it.valueRef() = log1p(double(it.value()) / colSums[k] * scale_factor);
    }
  }
  return data;
}