feat: implement default dimension reduction functions for Seurat objects

Author: pwwang

NAMESPACE

@@ -60,7 +60,6 @@ export(top)
 export(uniq)
 import(R6)
 importFrom(SeuratObject,"Idents<-")
-importFrom(SeuratObject,DefaultDimReduc)
 importFrom(SeuratObject,Embeddings)
 importFrom(SeuratObject,GetAssayData)
 importFrom(SeuratObject,Graphs)

R/celldimplot.R

@@ -21,7 +21,7 @@
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @export
 #' @seealso [scplotter::CellStatPlot()] [scplotter::CellVelocityPlot()]
-#' @importFrom SeuratObject DefaultDimReduc Embeddings Graphs Reductions Idents
+#' @importFrom SeuratObject Embeddings Graphs Reductions Idents
 #' @importFrom plotthis DimPlot
 #' @details
 #' See
@@ -268,7 +268,7 @@ CellDimPlot.Seurat <- function(
         is.null(group_by) || is.null(ident) || identical(group_by, ident))
     group_by <- group_by %||% ident
 
-    reduction <- reduction %||% DefaultDimReduc(object)
+    reduction <- reduction %||% default_dimreduc(object)
 
     if (!reduction %in% Reductions(object)) {
         stop("The object does not have reduction:", reduction)
@@ -397,7 +397,7 @@ CellDimPlot.H5File <- function(
 #' @return A ggplot object
 #' @export
 #' @seealso [scplotter::CellDimPlot()]
-#' @importFrom SeuratObject DefaultDimReduc Embeddings Reductions
+#' @importFrom SeuratObject Embeddings Reductions
 #' @importFrom plotthis VelocityPlot
 #' @details See:
 #' * <https://pwwang.github.io/scplotter/articles/Working_with_anndata_h5ad_files.html>

R/featurestatplot.R

@@ -212,7 +212,7 @@
 #' @return A ggplot object or a list if `combine` is FALSE
 #' @export
 #' @importFrom rlang %||%
-#' @importFrom SeuratObject GetAssayData Embeddings DefaultDimReduc Graphs Reductions Idents
+#' @importFrom SeuratObject GetAssayData Embeddings Graphs Reductions Idents
 #' @importFrom plotthis ViolinPlot BoxPlot BarPlot DotPlot RidgePlot FeatureDimPlot Heatmap CorPlot CorPairsPlot
 #' @details
 #' See:
@@ -567,7 +567,7 @@ FeatureStatPlot.Seurat <- function(
     stopifnot("[FeatureStatPlot] 'spat_unit' and 'feat_type' should not be used for Seurat object." = is.null(spat_unit) && is.null(feat_type))
 
     reduction <- reduction %||% (
-        if(is.null(Reductions(object))) NULL else DefaultDimReduc(object)
+        if(is.null(Reductions(object))) NULL else default_dimreduc(object)
     )
     # dim plot may use expression for highlighting cells
     # Heatmap may use other variables as annotations, but shrinking only includes minimal columns

R/utils.R

@@ -220,3 +220,51 @@ do_call <- function(fn, args, quote = FALSE, envir = parent.frame()) {
         enclos = envir
     )
 }
+
+#' Set default dimension reduction for Seurat object
+#'
+#' @details
+#' `DefaultDimReduc<-` was just introduced in Seurat v5.4.0
+#' See: https://github.com/satijalab/seurat-object/pull/268
+#' and https://github.com/satijalab/seurat-object/releases/tag/v5.4.0
+#' This function is a fallback for older Seurat versions that do not have this setter function.
+#' It will simply save the default dimension reduction name in the Seurat object's misc slot under `DefaultDimReduc`.
+#' When the setter function is available, it will use that instead.
+#'
+#' @param object Seurat object to modify
+#' @param value Name of the default dimension reduction to set
+#' @return Modified Seurat object with updated default dimension reduction
+#' @keywords internal
+`default_dimreduc<-` <- function(object, value) {
+    if (exists("DefaultDimReduc<-", where = asNamespace("SeuratObject"), mode = "function")) {
+        # Use the official setter if available
+        get("DefaultDimReduc<-", envir = asNamespace("SeuratObject"))(object, value)
+    } else {
+        # Fallback: store in misc slot
+        object@misc$DefaultDimReduc <- value
+    }
+    return(object)
+}
+
+#' Get default dimension reduction for Seurat object
+#'
+#' @details
+#' `DefaultDimReduc` was just introduced in Seurat v5.4.0.
+#' This function will first check if we have `DefaultDimReduc` value in the misc slot (set by our fallback setter),
+#' and if not, it will try to call the official `DefaultDimReduc` getter function. If that also fails, it will return NULL.
+#'
+#' @param object Seurat object to query
+#' @return Name of the default dimension reduction, or NULL if not set
+#' @keywords internal
+`default_dimreduc` <- function(object) {
+    # If we have SeuratObject >= 5.4.0, we can use the official getter
+    if (exists("DefaultDimReduc<-", where = asNamespace("SeuratObject"), mode = "function")) {
+        return(get("DefaultDimReduc", envir = asNamespace("SeuratObject"))(object))
+    }
+    # Fallback: check misc slot
+    if (!is.null(object@misc$DefaultDimReduc)) {
+        return(object@misc$DefaultDimReduc)
+    }
+    # Try to call official getter, may return NULL if not set
+    return(SeuratObject::DefaultDimReduc(object))
+}