Fix best matrix selection when matrix is sparse

Author: fspecque

R/RcppExports.R

@@ -1,7 +1,11 @@
 # Generated by using Rcpp::compileAttributes() -> do not edit by hand
 # Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
 
-n_zeros_mat <- function(mat) {
-    .Call(`_SeuratIntegrate_n_zeros_mat`, mat)
+n_zeros_dense_mat <- function(mat) {
+    .Call(`_SeuratIntegrate_n_zeros_dense_mat`, mat)
+}
+
+n_zeros_sparse_mat <- function(mat) {
+    .Call(`_SeuratIntegrate_n_zeros_sparse_mat`, mat)
 }
 

R/utils.R

@@ -743,6 +743,14 @@ could.be.connectivity.Matrix <- function(object, check.symmetry = T) {
 }
 #' @keywords internal
 #' @noRd
+n_zeros_mat <- function(mat) {
+  n <- if(is.matrix(mat)) n_zeros_dense_mat(mat)
+       else if (inherits(mat, what = "sparseMatrix")) n_zeros_sparse_mat(mat)
+       else tryCatch(sum(mat == 0, na.rm = TRUE), error = function(e) NA)
+  return(n)
+}
+#' @keywords internal
+#' @noRd
 choose_matrix_format <- function(mat) {
   max_int_32bit <- 2^31 - 1
   if (all(c(ncol(mat), nrow(mat)) <= max_int_32bit)) { # should always be TRUE

src/RcppExports.cpp

@@ -11,20 +11,32 @@ Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
 Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
 #endif
 
-// n_zeros_mat
-int64_t n_zeros_mat(const arma::mat& mat);
-RcppExport SEXP _SeuratIntegrate_n_zeros_mat(SEXP matSEXP) {
+// n_zeros_dense_mat
+int64_t n_zeros_dense_mat(const arma::mat& mat);
+RcppExport SEXP _SeuratIntegrate_n_zeros_dense_mat(SEXP matSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< const arma::mat& >::type mat(matSEXP);
-    rcpp_result_gen = Rcpp::wrap(n_zeros_mat(mat));
+    rcpp_result_gen = Rcpp::wrap(n_zeros_dense_mat(mat));
+    return rcpp_result_gen;
+END_RCPP
+}
+// n_zeros_sparse_mat
+int64_t n_zeros_sparse_mat(const arma::sp_mat& mat);
+RcppExport SEXP _SeuratIntegrate_n_zeros_sparse_mat(SEXP matSEXP) {
+BEGIN_RCPP
+    Rcpp::RObject rcpp_result_gen;
+    Rcpp::RNGScope rcpp_rngScope_gen;
+    Rcpp::traits::input_parameter< const arma::sp_mat& >::type mat(matSEXP);
+    rcpp_result_gen = Rcpp::wrap(n_zeros_sparse_mat(mat));
     return rcpp_result_gen;
 END_RCPP
 }
 
 static const R_CallMethodDef CallEntries[] = {
-    {"_SeuratIntegrate_n_zeros_mat", (DL_FUNC) &_SeuratIntegrate_n_zeros_mat, 1},
+    {"_SeuratIntegrate_n_zeros_dense_mat", (DL_FUNC) &_SeuratIntegrate_n_zeros_dense_mat, 1},
+    {"_SeuratIntegrate_n_zeros_sparse_mat", (DL_FUNC) &_SeuratIntegrate_n_zeros_sparse_mat, 1},
     {NULL, NULL, 0}
 };
 

src/n_zeros_matrix.cpp

@@ -2,8 +2,14 @@
 using namespace Rcpp;
 
 // [[Rcpp::export]]
-int64_t n_zeros_mat(const arma::mat &mat) {
+int64_t n_zeros_dense_mat(const arma::mat &mat) {
   int64_t count = arma::accu(mat == 0);
   return count;
 }
 
+// [[Rcpp::export]]
+int64_t n_zeros_sparse_mat(const arma::sp_mat &mat) {
+  int64_t count = mat.n_elem - mat.n_nonzero;
+  return count;
+}
+