Merge pull request satijalab#179 from satijalab/fix/RPCAFix

preserve reduction for rpca after recent changes to DietSeurat

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 3.0.3.9036
-Date: 2019-08-16
+Version: 3.0.3.9037
+Date: 2019-08-18
 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 Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
 Authors@R: c(

R/integration.R

@@ -240,13 +240,14 @@ FindIntegrationAnchors <- function(
         scale.data = TRUE,
         dimreducs = reduction
       )
-
       # suppress key duplication warning
       suppressWarnings(object.1[["ToIntegrate"]] <- object.1[[assay[i]]])
       DefaultAssay(object = object.1) <- "ToIntegrate"
+      slot(object = object.1[[reduction]], name = "assay.used") <- "ToIntegrate"
       object.1 <- DietSeurat(object = object.1, assays = "ToIntegrate", scale.data = TRUE, dimreducs = reduction)
       suppressWarnings(object.2[["ToIntegrate"]] <- object.2[[assay[j]]])
       DefaultAssay(object = object.2) <- "ToIntegrate"
+      slot(object = object.2[[reduction]], name = "assay.used") <- "ToIntegrate"
       object.2 <- DietSeurat(object = object.2, assays = "ToIntegrate", scale.data = TRUE, dimreducs = reduction)
       object.pair <- switch(
         EXPR = reduction,