add seurat v5 compatability

jackbibby1 · Feb 12, 2024 · 27b829a · 27b829a
1 parent 04aa7d7
commit 27b829a
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Showing 6 changed files with 38 additions and 8 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: SCPA
 Title: Single Cell Pathway Analysis
-Version: 1.5.4
+Version: 1.6
 Authors@R: 
     c(person(given = "Jack", family = "Bibby", email = "[email protected]", role = c("aut", "cre")),
       person(given = "Divyansh", family = "Agarwal", role = c("aut")))

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,10 @@
+## SCPA v1.6
+
+#### Major changes
+
+Updated compatability with Seurat v5
+  - Specify Seurat version in `compare_seurat()` and `seurat_extract()` with `seurat_v5 = TRUE` option
+
 ## SCPA v1.5.4
 
 ### Minor changes

diff --git a/R/CompareSeurat.R b/R/CompareSeurat.R
@@ -52,6 +52,7 @@ compare_seurat <- function(seurat_object,
                            downsample = 500,
                            min_genes = 15,
                            max_genes = 500,
+                           seurat_v5 = FALSE,
                            parallel = FALSE,
                            cores = NULL) {
 
@@ -68,7 +69,8 @@ compare_seurat <- function(seurat_object,
       samples[[i]] <- seurat_extract(seurat_object,
                                      assay = assay,
                                      meta1 = group1,
-                                     value_meta1 = i)
+                                     value_meta1 = i,
+                                     seurat_v5 = seurat_v5)
     }
   }
 
@@ -80,7 +82,8 @@ compare_seurat <- function(seurat_object,
                                      meta1 = group1,
                                      value_meta1 = i,
                                      meta2 = group2,
-                                     value_meta2 = group2_population)
+                                     value_meta2 = group2_population,
+                                     seurat_v5 = seurat_v5)
     }
   }
 

diff --git a/R/SeuratExtract.R b/R/SeuratExtract.R
@@ -31,11 +31,20 @@ seurat_extract <- function(seu_obj,
                            value_meta1 = NULL,
                            meta2 = NULL,
                            value_meta2 = NULL,
-                           pseudocount = 0.001) {
+                           pseudocount = 0.001,
+                           seurat_v5 = FALSE) {
+
+  if (seurat_v5 == FALSE) {
+    message("Expecting Seurat object < version 5. If using v5 object, specify seurat_v5 = T")
+  }
 
   if (is.null(meta1) && is.null(meta2)) {
     message("No metadata selected. Will convert whole Seurat object to matrix")
-    seu_obj <- as.matrix(Seurat::GetAssay(seu_obj, assay)@data) + pseudocount
+    if (seurat_v5 == FALSE) {
+      seu_obj <- as.matrix(Seurat::GetAssay(seu_obj, assay)@data) + pseudocount
+    } else {
+      seu_obj <- as.matrix(SeuratObject::LayerData(seu_obj, assay = assay, layer = "data")) + pseudocount
+    }
     message("Extracting data from the ", assay, " assay")
     return(seu_obj)
   }
@@ -44,7 +53,11 @@ seurat_extract <- function(seu_obj,
     message(paste0("Extracting cells where ", meta1, " == ", value_meta1))
     met_1 <- Seurat::FetchData(object = seu_obj, vars = meta1)
     seu_obj <- seu_obj[, which(met_1 == value_meta1)]
-    seu_obj <- as.matrix(Seurat::GetAssay(seu_obj, assay)@data) + pseudocount
+    if (seurat_v5 == FALSE) {
+      seu_obj <- as.matrix(Seurat::GetAssay(seu_obj, assay)@data) + pseudocount
+    } else {
+      seu_obj <- as.matrix(SeuratObject::LayerData(seu_obj, assay = assay, layer = "data")) + pseudocount
+    }
     message("Extracting data from the ", assay, " assay")
     return(seu_obj)
   }
@@ -55,11 +68,15 @@ seurat_extract <- function(seu_obj,
     met_1 <- Seurat::FetchData(object = seu_obj, vars = meta1)
     met_2 <- Seurat::FetchData(object = seu_obj, vars = meta2)
     seu_obj <- seu_obj[, which(met_1 == value_meta1 & met_2 == value_meta2)]
-    seu_obj <- as.matrix(Seurat::GetAssay(seu_obj, assay)@data) + pseudocount
+    if (seurat_v5 == FALSE) {
+      seu_obj <- as.matrix(Seurat::GetAssay(seu_obj, assay)@data) + pseudocount
+    } else {
+      seu_obj <- as.matrix(SeuratObject::LayerData(seu_obj, assay = assay, layer = "data")) + pseudocount
+    }
     message("Extracting data from the ", assay, " assay")
     return(seu_obj)
   }
-}
 
+}
 
 
diff --git a/README.Rmd b/README.Rmd
@@ -28,6 +28,7 @@ knitr::opts_chunk$set(
 1. [Improvements/changes/updates](https://jackbibby1.github.io/SCPA/news/index.html) to SCPA
 
 ### Recent updates
+- Compatability with Seurat v5 objects to use the layer system in `seurat_extract()` and `compare_seurat()` (v1.6) through specifying `seurat_v5 = TRUE`. Currently default is FALSE, but this will change after a while
 - Ability to specify [multiple gmt files](https://jackbibby1.github.io/SCPA/articles/using_gene_sets.html#using-a-gmt-file) as your pathway input (v1.5.2)
 - [Parallel processing](https://jackbibby1.github.io/SCPA/articles/parallel_implementation.html) implemented to speed up analyses (v1.5.0)
 - Much more efficient usage of memory, so this shouldn't be limiting (v1.3.0)

diff --git a/README.md b/README.md
@@ -22,6 +22,8 @@
 
 ### Recent updates
 
+- Compatability with Seurat v5 objects to use the layer system in
+  `seurat_extract()` and `compare_seurat()` (v1.6)
 - Ability to specify [multiple gmt
   files](https://jackbibby1.github.io/SCPA/articles/using_gene_sets.html#using-a-gmt-file)
   as your pathway input (v1.5.2)