1. celda
  2. src
  3. matrixNorm.cpp
Browse code

Coverted DecontX C code to use RcppEigen instead of RcppArmadillo as it was faster and didn't prodcue warnings when checking

Joshua D. Campbell authored on 02/04/2020 20:56:09
Showing 1 changed files
src/matrixNorm.cpp
History View file @ d671d202
... ... 
@@ -1,4 +1,4 @@
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-// [[Rcpp::depends(RcppEigen)]]
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+// [[Rcpp::depends(Rcpp)]]
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 #include <Rcpp.h>
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 using namespace Rcpp ;
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... ... 
@@ -27,10 +27,6 @@ SEXP fastNormProp(NumericMatrix R_counts, double R_alpha) {
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 }
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-// [[Rcpp::depends(RcppEigen)]]
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-#include <Rcpp.h>
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-using namespace Rcpp ;
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-
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 //' Fast normalization for numeric matrix
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 //'
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 //' @param R_counts An integer matrix
... ... 
@@ -56,10 +52,6 @@ SEXP fastNormPropLog(NumericMatrix R_counts, double R_alpha) {
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 }
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-// [[Rcpp::depends(RcppEigen)]]
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-#include <Rcpp.h>
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-using namespace Rcpp ;
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-
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 //' Fast normalization for numeric matrix
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 //'
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 //' @param R_counts An integer matrix
... ... 
@@ -86,10 +78,6 @@ SEXP fastNormPropSqrt(NumericMatrix R_counts, double R_alpha) {
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-// [[Rcpp::depends(RcppEigen)]]
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-#include <Rcpp.h>
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-using namespace Rcpp ;
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-
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 //' get row and column indices of none zero elements in the matrix
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 //'
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 //' @param R_counts A matrix
Browse code

Moved new Nonezero cpp function to different file. Fixed celda_heatmap bug causing vignette building to fail. Renamed vignettes. Started new draft of decontX vignette.

Joshua D. Campbell authored on 13/03/2020 00:31:44
Showing 1 changed files
src/matrixNorm.cpp
History View file @ 80f6cc99
... ... 
@@ -84,3 +84,47 @@ SEXP fastNormPropSqrt(NumericMatrix R_counts, double R_alpha) {
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   return Rcpp::wrap(res);
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 }
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+
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+
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+// [[Rcpp::depends(RcppEigen)]]
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+#include <Rcpp.h>
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+using namespace Rcpp ;
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+
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+//' get row and column indices of none zero elements in the matrix
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+//'
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+//' @param R_counts A matrix
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+//' @return An integer matrix where each row is a row, column indices pair
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+// [[Rcpp::export]]
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+SEXP nonzero(NumericMatrix R_counts) {
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+
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+  IntegerVector row(1);
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+  IntegerVector col(1);
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+  NumericVector val(1);
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+
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+  int nR = R_counts.nrow();
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+  int nC = R_counts.ncol();
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+  double x;
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+
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+  for (int c = 0; c < nC; c++) {
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+    for (int r = 0; r < nR; r++) {
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+      x = R_counts[c * nR + r];
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+      if (x != 0) {
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+        row.push_back(r + 1);
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+        col.push_back(c + 1);
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+        val.push_back(x);
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+      }
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+    }
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+  }
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+
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+  row.erase(0);
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+  col.erase(0);
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+  val.erase(0);
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+
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+  List res;
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+  res["row"] = row;
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+  res["col"] = col;
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+  res["val"] = val;
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+
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+  return(res);
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+}
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+
Browse code

stop if division by 0

87875172 authored on 11/04/2019 20:05:22
Showing 1 changed files
src/matrixNorm.cpp
History View file @ 57b334d4
... ... 
@@ -46,6 +46,9 @@ SEXP fastNormPropLog(NumericMatrix R_counts, double R_alpha) {
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   // Normalize cell counts to proportions after adding pseudocount
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   double alpha_tot = R_counts.nrow() * R_alpha;
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   for (int i = 0; i < R_counts.ncol(); ++i) {
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+    if (cs[i] + alpha_tot == 0) {
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+      stop("Division by 0. Make sure colSums of counts does not contain 0 after rounding counts to integers.");
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+    }
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     res(_,i) = log((R_counts(_,i) + R_alpha) / (cs[i] + alpha_tot));
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   }
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... ... 
@@ -72,6 +75,9 @@ SEXP fastNormPropSqrt(NumericMatrix R_counts, double R_alpha) {
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   // Normalize cell counts to proportions after adding pseudocount
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   double alpha_tot = R_counts.nrow() * R_alpha;
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   for (int i = 0; i < R_counts.ncol(); ++i) {
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+    if (cs[i] + alpha_tot == 0) {
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+      stop("Division by 0. Make sure colSums of counts does not contain 0 after rounding counts to integers.");
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+    }
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     res(_,i) = sqrt((R_counts(_,i) + R_alpha) / (cs[i] + alpha_tot));
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   }
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Browse code

fix division by 0 error in fastNormProp

87875172 authored on 11/04/2019 20:03:49
Showing 1 changed files
src/matrixNorm.cpp
History View file @ 977ae3ac
... ... 
@@ -17,6 +17,9 @@ SEXP fastNormProp(NumericMatrix R_counts, double R_alpha) {
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   // Normalize cell counts to proportions after adding pseudocount
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   double alpha_tot = R_counts.nrow() * R_alpha;
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   for (int i = 0; i < R_counts.ncol(); ++i) {
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+    if (cs[i] + alpha_tot == 0) {
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+      stop("Division by 0. Make sure colSums of counts does not contain 0 after rounding counts to integers.");
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+    }
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     res(_,i) = (R_counts(_,i) + R_alpha) / (cs[i] + alpha_tot);
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   }
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Browse code

Added Rcpp functions for fast matrix normalization.

Former-commit-id: 483084aa24c74526bc5f6004e6059b3810b73ab2

Joshua D. Campbell authored on 27/08/2018 19:54:54
Showing 1 changed files
src/matrixNorm.cpp
History View file @ cd921f84
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,77 @@
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+// [[Rcpp::depends(RcppEigen)]]
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+#include <Rcpp.h>
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+using namespace Rcpp ;
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+
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+//' Fast normalization for numeric matrix
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+//'
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+//' @param R_counts An integer matrix
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+//' @param R_alpha A double value to be added to the matrix as a pseudocount
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+//' @return A numeric matrix where the columns have been normalized to proportions
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+// [[Rcpp::export]]
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+SEXP fastNormProp(NumericMatrix R_counts, double R_alpha) {
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+
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+  // Get colSums and instantiate new matrix
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+  NumericVector cs = colSums(R_counts);
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+  NumericMatrix res = NumericMatrix(R_counts.nrow(), R_counts.ncol());
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+
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+  // Normalize cell counts to proportions after adding pseudocount
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+  double alpha_tot = R_counts.nrow() * R_alpha;
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+  for (int i = 0; i < R_counts.ncol(); ++i) {
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+    res(_,i) = (R_counts(_,i) + R_alpha) / (cs[i] + alpha_tot);
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+  }
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+
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+  return Rcpp::wrap(res);
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+}
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+
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+
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+// [[Rcpp::depends(RcppEigen)]]
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+#include <Rcpp.h>
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+using namespace Rcpp ;
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+
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+//' Fast normalization for numeric matrix
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+//'
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+//' @param R_counts An integer matrix
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+//' @param R_alpha A double value to be added to the matrix as a pseudocount
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+//' @return A numeric matrix where the columns have been normalized to proportions
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+// [[Rcpp::export]]
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+SEXP fastNormPropLog(NumericMatrix R_counts, double R_alpha) {
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+
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+  // Get colSums and instantiate new matrix
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+  NumericVector cs = colSums(R_counts);
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+  NumericMatrix res = NumericMatrix(R_counts.nrow(), R_counts.ncol());
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+
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+  // Normalize cell counts to proportions after adding pseudocount
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+  double alpha_tot = R_counts.nrow() * R_alpha;
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+  for (int i = 0; i < R_counts.ncol(); ++i) {
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+    res(_,i) = log((R_counts(_,i) + R_alpha) / (cs[i] + alpha_tot));
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+  }
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+
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+  return Rcpp::wrap(res);
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+}
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+
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+
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+// [[Rcpp::depends(RcppEigen)]]
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+#include <Rcpp.h>
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+using namespace Rcpp ;
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+
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+//' Fast normalization for numeric matrix
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+//'
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+//' @param R_counts An integer matrix
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+//' @param R_alpha A double value to be added to the matrix as a pseudocount
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+//' @return A numeric matrix where the columns have been normalized to proportions
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+// [[Rcpp::export]]
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+SEXP fastNormPropSqrt(NumericMatrix R_counts, double R_alpha) {
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+
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+  // Get colSums and instantiate new matrix
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+  NumericVector cs = colSums(R_counts);
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+  NumericMatrix res = NumericMatrix(R_counts.nrow(), R_counts.ncol());
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+
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+  // Normalize cell counts to proportions after adding pseudocount
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+  double alpha_tot = R_counts.nrow() * R_alpha;
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+  for (int i = 0; i < R_counts.ncol(); ++i) {
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+    res(_,i) = sqrt((R_counts(_,i) + R_alpha) / (cs[i] + alpha_tot));
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+  }
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+
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+  return Rcpp::wrap(res);
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+}
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+