satijalab · mojaveazure · Jun 11, 2021 · Apr 30, 2021 · May 25, 2021 · May 26, 2021
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.0.2.9002
-Date: 2021-05-28
+Version: 4.0.2.9003
+Date: 2021-06-01
 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(

diff --git a/R/objects.R b/R/objects.R
@@ -1106,15 +1106,17 @@ as.Seurat.SingleCellExperiment <- function(
     DefaultAssay(object = object) <- assay
     # add feature level meta data
     md <- SingleCellExperiment::rowData(x = x)
-    # replace underscores
-    rownames(x = md) <- gsub(pattern = "_", replacement = "-", x = rownames(x = md))
-    md <- as.data.frame(x = md)
-    # ensure order same as data
-    md <- md[rownames(x = object[[assay]]), ]
-    object[[assay]] <- AddMetaData(
-      object = object[[assay]],
-      metadata = md
-    )
+    if (ncol(x = md) > 0) {
+      # replace underscores
+      rownames(x = md) <- gsub(pattern = "_", replacement = "-", x = rownames(x = md))
+      md <- as.data.frame(x = md)
+      # ensure order same as data
+      md <- md[rownames(x = object[[assay]]), ]
+      object[[assay]] <- AddMetaData(
+        object = object[[assay]],
+        metadata = md
+      )
+    }
     Idents(object = object) <- project
     # Get DimReduc information, add underscores if needed and pull from different alt EXP
     if (length(x = SingleCellExperiment::reducedDimNames(x = x)) > 0) {
@@ -1174,17 +1176,17 @@ as.SingleCellExperiment.Seurat <- function(x, assay = NULL, ...) {
   }
   experiments <- list()
   for (assayn in assay) {
-  assays = list(
-    counts = GetAssayData(object = x, assay = assayn, slot = "counts"),
-    logcounts = GetAssayData(object = x, assay = assayn, slot = "data"))
+    assays = list(
+      counts = GetAssayData(object = x, assay = assayn, slot = "counts"),
+      logcounts = GetAssayData(object = x, assay = assayn, slot = "data"))
     assays <- assays[sapply(X = assays, FUN = nrow) != 0]
     sume <- SummarizedExperiment::SummarizedExperiment(assays = assays)
     experiments[[assayn]] <- sume
   }
   # create one single cell experiment
   sce <- as(object = experiments[[1]], Class = "SingleCellExperiment")
-  sce <- SingleCellExperiment::SingleCellExperiment(sce, altExps = experiments)
   orig.exp.name <- names(x = experiments[1])
+  sce <- SingleCellExperiment::SingleCellExperiment(sce, altExps = experiments)
   sce <- SingleCellExperiment::swapAltExp(
     x = sce,
     name = orig.exp.name,
@@ -1210,13 +1212,15 @@ 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)) {
+    if (assay.used %in% SingleCellExperiment::altExpNames(x = sce) & assay.used != orig.exp.name) {
       sce <- SingleCellExperiment::swapAltExp(
         x = sce,
         name = assay.used,
         saved = orig.exp.name
       )
-      SingleCellExperiment::reducedDim(x = sce, type = toupper(x = dr)) <- Embeddings(object = x[[dr]])
+    }
+    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) {
       sce <- SingleCellExperiment::swapAltExp(
         x = sce,
         name = orig.exp.name,

diff --git a/vignettes/conversion_vignette.Rmd b/vignettes/conversion_vignette.Rmd
@@ -31,6 +31,9 @@ knitr::opts_chunk$set(
 )
 ```
 
+```{r, include = FALSE, cache=FALSE}
+options(SeuratData.repo.use = "http://satijalab04.nygenome.org")
+```
 In this vignette, we demonstrate the ability to convert between Seurat objects, SingleCellExperiment objects, and anndata objects. 
 
 ```{r packages}
@@ -41,6 +44,7 @@ library(Seurat)
 # install SeuratDisk from GitHub using the remotes package
 # remotes::install_github(repo = 'mojaveazure/seurat-disk', ref = 'develop')
 library(SeuratDisk)
+library(SeuratData)
 library(patchwork)
 ```
 
@@ -49,9 +53,9 @@ library(patchwork)
 [`SingleCellExperiment`](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html) is a class for storing single-cell experiment data, created by Davide Risso, Aaron Lun, and Keegan Korthauer, and is used by many Bioconductor analysis packages. Here we demonstrate converting the Seurat object produced in our 3k PBMC tutorial to SingleCellExperiment for use with Davis McCarthy's [scater](https://bioconductor.org/packages/release/bioc/html/scater.html) package. 
 
 ```{r seurat_singlecell}
-# download from satija lab
-# https://www.dropbox.com/s/kwd3kcxkmpzqg6w/pbmc3k_final.rds?dl=0
-pbmc <- readRDS(file = '../data/pbmc3k_final.rds')
+# Use PBMC3K from SeuratData
+InstallData("pbmc3k")
+pbmc <- LoadData(ds = "pbmc3k", type = "pbmc3k.final")
 pbmc.sce <- as.SingleCellExperiment(pbmc)
 p1 <- plotExpression(pbmc.sce, features = 'MS4A1', x = 'ident') + theme(axis.text.x = element_text(angle = 45, hjust = 1))
 p2 <- plotPCA(pbmc.sce, colour_by = 'ident')