Add progress bar to SparseRowVarStd

bbimber · Jul 29, 2018 · b215b39 · b215b39
1 parent 058fe40
commit b215b39
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Showing 5 changed files with 19 additions and 9 deletions.
diff --git a/R/RcppExports.R b/R/RcppExports.R
@@ -57,8 +57,8 @@ SparseRowSd <- function(mat) {
     .Call('_Seurat_SparseRowSd', PACKAGE = 'Seurat', mat)
 }
 
-SparseRowVarStd <- function(mat, mu, sd, vmax) {
-    .Call('_Seurat_SparseRowVarStd', PACKAGE = 'Seurat', mat, mu, sd, vmax)
+SparseRowVarStd <- function(mat, mu, sd, vmax, display_progress) {
+    .Call('_Seurat_SparseRowVarStd', PACKAGE = 'Seurat', mat, mu, sd, vmax, display_progress)
 }
 
 FastExpVar <- function(mat, display_progress) {

diff --git a/R/preprocessing.R b/R/preprocessing.R
@@ -1076,7 +1076,8 @@ FindVariableFeaturesNew.default <- function(
   hvf.info$variance.standardized <- SparseRowVarStd(mat = object, 
                                                     mu = hvf.info$mean, 
                                                     sd = sqrt(hvf.info$variance.expected), 
-                                                    vmax = clip.max)
+                                                    vmax = clip.max,
+                                                    display_progress = verbose)
   return(hvf.info)
 }
 

diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -189,16 +189,17 @@ BEGIN_RCPP
 END_RCPP
 }
 // SparseRowVarStd
-Eigen::VectorXd SparseRowVarStd(Eigen::SparseMatrix<double> mat, Eigen::VectorXd mu, Eigen::VectorXd sd, double vmax);
-RcppExport SEXP _Seurat_SparseRowVarStd(SEXP matSEXP, SEXP muSEXP, SEXP sdSEXP, SEXP vmaxSEXP) {
+Eigen::VectorXd SparseRowVarStd(Eigen::SparseMatrix<double> mat, Eigen::VectorXd mu, Eigen::VectorXd sd, double vmax, bool display_progress);
+RcppExport SEXP _Seurat_SparseRowVarStd(SEXP matSEXP, SEXP muSEXP, SEXP sdSEXP, SEXP vmaxSEXP, SEXP display_progressSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;
     Rcpp::RNGScope rcpp_rngScope_gen;
     Rcpp::traits::input_parameter< Eigen::SparseMatrix<double> >::type mat(matSEXP);
     Rcpp::traits::input_parameter< Eigen::VectorXd >::type mu(muSEXP);
     Rcpp::traits::input_parameter< Eigen::VectorXd >::type sd(sdSEXP);
     Rcpp::traits::input_parameter< double >::type vmax(vmaxSEXP);
-    rcpp_result_gen = Rcpp::wrap(SparseRowVarStd(mat, mu, sd, vmax));
+    Rcpp::traits::input_parameter< bool >::type display_progress(display_progressSEXP);
+    rcpp_result_gen = Rcpp::wrap(SparseRowVarStd(mat, mu, sd, vmax, display_progress));
     return rcpp_result_gen;
 END_RCPP
 }
@@ -321,7 +322,7 @@ static const R_CallMethodDef CallEntries[] = {
     {"_Seurat_FastExpMean", (DL_FUNC) &_Seurat_FastExpMean, 2},
     {"_Seurat_SparseRowVar", (DL_FUNC) &_Seurat_SparseRowVar, 2},
     {"_Seurat_SparseRowSd", (DL_FUNC) &_Seurat_SparseRowSd, 1},
-    {"_Seurat_SparseRowVarStd", (DL_FUNC) &_Seurat_SparseRowVarStd, 4},
+    {"_Seurat_SparseRowVarStd", (DL_FUNC) &_Seurat_SparseRowVarStd, 5},
     {"_Seurat_FastExpVar", (DL_FUNC) &_Seurat_FastExpVar, 2},
     {"_Seurat_FastLogVMR", (DL_FUNC) &_Seurat_FastLogVMR, 2},
     {"_Seurat_RowSumOfSquares", (DL_FUNC) &_Seurat_RowSumOfSquares, 1},

diff --git a/src/data_manipulation.cpp b/src/data_manipulation.cpp
@@ -345,12 +345,19 @@ Eigen::VectorXd SparseRowSd(Eigen::SparseMatrix<double> mat){
 Eigen::VectorXd SparseRowVarStd(Eigen::SparseMatrix<double> mat, 
                                 Eigen::VectorXd mu, 
                                 Eigen::VectorXd sd,
-                                double vmax){
+                                double vmax,
+                                bool display_progress){
   mat = mat.transpose();
   Eigen::VectorXd allVars(mat.cols());
   allVars.fill(0);
 
+  if(display_progress == true){
+    Rcpp::Rcerr << "Calculating feature variances of standardized and clipped values" << std::endl;
+  }
+  Progress p(mat.outerSize(), display_progress);
+
   for (int k=0; k<mat.outerSize(); ++k){
+    p.increment();
     if (sd(k) == 0) continue;
     double colSum = 0;
     int nZero = mat.rows();

diff --git a/src/data_manipulation.h b/src/data_manipulation.h
@@ -41,7 +41,8 @@ Eigen::VectorXd SparseRowSd(Eigen::SparseMatrix<double> mat);
 Eigen::VectorXd SparseRowVarStd(Eigen::SparseMatrix<double> mat, 
                                 Eigen::VectorXd mu, 
                                 Eigen::VectorXd sd,
-                                double vmax);
+                                double vmax,
+                                bool display_progress);
 NumericVector RowSumOfSquares(const NumericMatrix x);
 NumericVector RowVar(Eigen::Map<Eigen::MatrixXd> x);
 int IntersectLength(std::vector<int> a, std::vector<int> b);