v2.1.5

v5 seurat handling
ncborcherding · Oct 23, 2024 · 850adbe · 850adbe
1 parent d89f74e
commit 850adbe
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Showing 4 changed files with 15 additions and 5 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: escape
 Title: Easy single cell analysis platform for enrichment
-Version: 2.1.4
-Date: 2024-09-19
+Version: 2.1.5
+Date: 2024-10-23
 Authors@R: c(
     person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "[email protected]"),
     person(given = "Jared", family = "Andrews", role = c("aut"), email = "[email protected]"),

diff --git a/NAMESPACE b/NAMESPACE
@@ -29,6 +29,7 @@ importFrom(Matrix,colSums)
 importFrom(MatrixGenerics,rowSds)
 importFrom(MatrixGenerics,rowSums2)
 importFrom(SeuratObject,Assays)
+importFrom(SeuratObject,CreateAssay5Object)
 importFrom(SeuratObject,CreateAssayObject)
 importFrom(SeuratObject,CreateDimReducObject)
 importFrom(SeuratObject,Idents)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# escape VERSION 2.1.5 (2024-10-23)
+
+* update handling of v5 Seurat versus <v5 Seurat Objects
+
 # escape VERSION 2.1.4 (2024-09-13)
 
 * update ```densityEnrichment()``` GSVA function pull

diff --git a/R/utils.R b/R/utils.R
@@ -175,13 +175,18 @@ is_seurat_or_se_object <- function(obj) {
 }
 
 #Add the values to single cell object
-#' @importFrom SeuratObject CreateAssayObject
+#' @importFrom SeuratObject CreateAssayObject CreateAssay5Object
 #' @importFrom SummarizedExperiment SummarizedExperiment assays<-
 #' @importFrom SingleCellExperiment altExps altExp<- 
 .adding.Enrich <- function(sc, enrichment, enrichment.name) {
   if (inherits(sc, "Seurat")) {
-    new.assay <- suppressWarnings(CreateAssayObject(
-                                  data = as.matrix(t(enrichment))))
+    if (as.numeric(substr(sc@version,1,1)) == 5) {
+      new.assay <- suppressWarnings(CreateAssay5Object(
+                                    data = as.matrix(t(enrichment))))
+    } else {
+      new.assay <- suppressWarnings(CreateAssayObject(
+                                    data = as.matrix(t(enrichment))))
+    }
 
     suppressWarnings(sc[[enrichment.name]] <- new.assay)
   } else if (inherits(sc, "SingleCellExperiment")) {