Merge pull request #25 from MartinLoza/SeuratV5_fix

Seurat v5 fix
MartinLoza · Nov 5, 2023 · 05d0e38 · 05d0e38
2 parents d6998e6 + 11337b4
commit 05d0e38
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Showing 6 changed files with 16 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: Canek
 Type: Package
 Title: Batch Correction of Single Cell Transcriptome Data
-Version: 0.2.3
+Version: 0.2.4
 Authors@R: c(
     person("Martin", "Loza", email = "martin.loza.lopez@gmail.com", role = c("aut", "cre"), 
         comment = c(ORCID = "0000-0002-3342-2643")),
@@ -20,7 +20,8 @@ Imports:
     fpc,
     bluster,
     igraph,
-    matrixStats
+    matrixStats,
+    utils
 Suggests:
     testthat (>= 2.1.0),
     Seurat,

diff --git a/NAMESPACE b/NAMESPACE
@@ -21,3 +21,4 @@ importFrom(stats,dist)
 importFrom(stats,kmeans)
 importFrom(stats,quantile)
 importFrom(stats,sd)
+importFrom(utils,packageVersion)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# Canek 0.2.4
+
+## Changes
+
+- Update Canek for compatibility with Seurat v5 ([#20](https://github.com/MartinLoza/Canek/issues/20))
+
 # Canek 0.2.3
 
 ## Changes

diff --git a/R/Canek-package.R b/R/Canek-package.R
@@ -5,6 +5,7 @@
 # roxygen namespace tags. Modify with care!
 ## usethis namespace: start
 #' @import numbers
+#' @importFrom utils packageVersion
 #' @importFrom stats dist kmeans sd quantile
 #' @importFrom igraph cluster_louvain membership mst graph_from_adjacency_matrix as_edgelist
 #' @importFrom bluster makeSNNGraph

diff --git a/R/RunCanek.R b/R/RunCanek.R
@@ -41,7 +41,10 @@ RunCanek.Seurat <- function(x, batches = NULL, slot = "data", assay = NULL, feat
   }
 
   counts <- lapply(obj, function(xx) {
-    Seurat::GetAssayData(xx, slot = slot, assay = assay)[features, ]
+    if (packageVersion("Seurat") >= "5.0.0")
+      Seurat::GetAssayData(xx, layer = slot, assay = assay)[features, ]
+    else
+      Seurat::GetAssayData(xx, slot = slot, assay = assay)[features, ]
   })
 
   counts <- Canek::CorrectBatches(counts, debug = debug, ...)

diff --git a/tests/testthat/test_RunCanek.R b/tests/testthat/test_RunCanek.R
@@ -24,7 +24,7 @@ y <- SingleCellExperiment::SingleCellExperiment(list(counts=m, logcounts=m))
 y$batch <- b
 
 # RunCanek.
-x <- RunCanek(x, "batch")
+x <- RunCanek(x, "batch", slot="counts")
 y <- RunCanek(y, "batch")
 z <- RunCanek(list(B1=m1, B2=m2), debug = TRUE)