Fixed conflict

campbio · Oct 3, 2021 · 8698668 · 8698668
2 parents c96bb98 + 588fa5c
commit 8698668
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Showing 3 changed files with 18 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -30,7 +30,7 @@ LinkingTo: Rcpp, RcppEigen
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 BugReports: https://github.com/campbio/celda/issues
 biocViews: SingleCell, GeneExpression, Clustering, Sequencing, Bayesian
 NeedsCompilation: yes
diff --git a/R/decon.R b/R/decon.R
@@ -507,8 +507,18 @@ setMethod(
       pseudocount = 1e-20
     )
 
-    # This part needs to be optimized
-    estRmat[seq(nrow(counts)), which(batch == bat)] <- estRmat.temp
+    # Speed up sparse matrix value assignment by cbind -> order recovery
+    allCol <- paste0("col_", seq_len(ncol(estRmat)))
+    colnames(estRmat) <- allCol
+
+    subCol <- paste0("col_", which(batch == bat))
+    colnames(estRmat.temp) <- subCol
+
+    estRmat <- estRmat[, !(allCol %in% subCol)]
+    estRmat <- cbind(estRmat, estRmat.temp)
+
+    # Recover order and set names
+    estRmat <- estRmat[, allCol]
     dimnames(estRmat) <- list(geneNames, allCellNames)
 
     resBatch[[bat]] <- list(

diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -6,6 +6,11 @@
 
 using namespace Rcpp;
 
+#ifdef RCPP_USE_GLOBAL_ROSTREAM
+Rcpp::Rostream<true>&  Rcpp::Rcout = Rcpp::Rcpp_cout_get();
+Rcpp::Rostream<false>& Rcpp::Rcerr = Rcpp::Rcpp_cerr_get();
+#endif
+
 // decontXEM
 Rcpp::List decontXEM(const Eigen::MappedSparseMatrix<double>& counts, const NumericVector& counts_colsums, const NumericVector& theta, const bool& estimate_eta, const NumericMatrix& eta, const NumericMatrix& phi, const IntegerVector& z, const bool& estimate_delta, const NumericVector& delta, const double& pseudocount);
 RcppExport SEXP _celda_decontXEM(SEXP countsSEXP, SEXP counts_colsumsSEXP, SEXP thetaSEXP, SEXP estimate_etaSEXP, SEXP etaSEXP, SEXP phiSEXP, SEXP zSEXP, SEXP estimate_deltaSEXP, SEXP deltaSEXP, SEXP pseudocountSEXP) {