Merge pull request satijalab#590 from satijalab/fix/SingleCellExperim…

…ent_assay Fix/single cell experiment assay
trn13 · Aug 6, 2021 · 60b977c · 60b977c
2 parents 434d918 + 1ab3106
commit 60b977c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.0.3.9013
-Date: 2021-07-30
+Version: 4.0.3.9014
+Date: 2021-08-06
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
 Authors@R: c(
@@ -57,7 +57,7 @@ Imports:
     png,
     RANN,
     RColorBrewer,
-    Rcpp,
+    Rcpp (>= 1.0.7),
     RcppAnnoy (>= 0.0.18),
     reticulate,
     rlang,

diff --git a/NEWS.md b/NEWS.md
@@ -16,6 +16,7 @@
 - Bug fix in `FindVariableFeatures()` when using `selection.method = "mvp"` and `binning.method = "equal_frequency"` ([#4712](https://github.com/satijalab/seurat/issues/4712))
 - Bug fix in `DoHeatmap()` to remove random characters from plot legend([#4660](https://github.com/satijalab/seurat/issues/4660))
 - Fix cell renaming in `RunCCA()`
+- Fix issue in SingleCellExperiment conversion where the mainExp would not be set properly
 
 ## Seurat 4.0.3 (2020-06-10)`
 ## Added

diff --git a/R/objects.R b/R/objects.R
@@ -1179,6 +1179,9 @@ as.SingleCellExperiment.Seurat <- function(x, assay = NULL, ...) {
   if (!all(assay %in% Assays(object = x))) {
     stop("One or more of the assays you are trying to convert is not in the Seurat object")
   }
+  if (DefaultAssay(object = x) %in% assay) {
+    assay <- union(DefaultAssay(object = x), assay)
+  }
   experiments <- list()
   for (assayn in assay) {
     assays <- list(
@@ -1230,15 +1233,16 @@ as.SingleCellExperiment.Seurat <- function(x, assay = NULL, ...) {
   }
   for (dr in FilterObjects(object = x, classes.keep = "DimReduc")) {
     assay.used <- DefaultAssay(object = x[[dr]])
-    if (assay.used %in% SingleCellExperiment::altExpNames(x = sce) & assay.used != orig.exp.name) {
+    swap.exp <- assay.used %in% SingleCellExperiment::altExpNames(x = sce) & assay.used != orig.exp.name
+    if (swap.exp) {
       sce <- SingleCellExperiment::swapAltExp(
         x = sce,
         name = assay.used,
         saved = orig.exp.name
       )
     }
     SingleCellExperiment::reducedDim(x = sce, type = toupper(x = dr)) <- Embeddings(object = x[[dr]])
-    if (assay.used %in% SingleCellExperiment::altExpNames(x = sce) & assay.used != orig.exp.name) {
+    if (swap.exp) {
       sce <- SingleCellExperiment::swapAltExp(
         x = sce,
         name = orig.exp.name,

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
+
 // RunModularityClusteringCpp
 IntegerVector RunModularityClusteringCpp(Eigen::SparseMatrix<double> SNN, int modularityFunction, double resolution, int algorithm, int nRandomStarts, int nIterations, int randomSeed, bool printOutput, std::string edgefilename);
 RcppExport SEXP _Seurat_RunModularityClusteringCpp(SEXP SNNSEXP, SEXP modularityFunctionSEXP, SEXP resolutionSEXP, SEXP algorithmSEXP, SEXP nRandomStartsSEXP, SEXP nIterationsSEXP, SEXP randomSeedSEXP, SEXP printOutputSEXP, SEXP edgefilenameSEXP) {