From 8ee10427aeb799d059628192e66a4426e255173c Mon Sep 17 00:00:00 2001
From: multitalk <xin_shao@zju.edu.cn>
Date: Fri, 14 Jun 2024 11:46:52 +0800
Subject: [PATCH] Update utils.R

#40
compatible with Seurat 5
---
 R/utils.R | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/R/utils.R b/R/utils.R
index ca84cb2..d3a4160 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -286,7 +286,17 @@
 .normalize_data <- function(rawdata) {
     rawdata <- Seurat::CreateSeuratObject(rawdata)
     rawdata <- Seurat::NormalizeData(rawdata, verbose = F)
-    rawdata <- rawdata[["RNA"]]@data
+    ver <- packageVersion("Seurat")
+    ver <- substr(ver,1,1)
+    if (ver >= 5) {
+        genenames <- rownames(rawdata)
+        cellnames <- colnames(rawdata)
+        rawdata <- rawdata[["RNA"]]@layers$data
+        rownames(rawdata) <- genenames
+        colnames(rawdata) <- cellnames
+    } else {
+        rawdata <- rawdata[["RNA"]]@data
+    }
     return(rawdata)
 }