Merge pull request satijalab#312 from satijalab/fix/renameassay

Update assay.used for DimReduc objects

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 3.1.4.9026
-Date: 2020-04-09
+Version: 3.1.4.9027
+Date: 2020-04-10
 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>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details. Please note:  SDMTools is available is available from the CRAN archives with install.packages("https://cran.rstudio.com//src/contrib/Archive/SDMTools/SDMTools_1.1-221.2.tar.gz", repos = NULL); it is not in the standard repositories.
 Authors@R: c(

R/objects.R

@@ -1309,6 +1309,12 @@ RenameAssays <- function(object, ...) {
       DefaultAssay(object = object) <- new
     }
     Key(object = object[[new]]) <- old.key
+    # change assay used in any dimreduc object
+    for (i in Reductions(object = object)) {
+      if (DefaultAssay(object = object[[i]]) == old) {
+        DefaultAssay(object = object[[i]]) <- new
+      }
+    }
     object[[old]] <- NULL
   }
   return(object)