Merge pull request #9625 from joesphbeller/master

Fix GroupCorrelation and GroupCorrelationPlot for Seurat V5 compatibility

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Seurat
-Version: 5.2.99.9000
+Version: 5.2.99.9001
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
 Authors@R: c(

NEWS.md

@@ -1,3 +1,8 @@
+# Unreleased
+
+## Changes
+- Fixed `GroupCorrelation` and `GroupCorrelationPlot` to be compatible with `SeuratObject` >= 5.0.0 ([#9625](https://github.com/satijalab/seurat/pull/9625))
+
 # Seurat 5.2.1 (2025-01-23)
 
 ## Changes

R/utilities.R

@@ -986,7 +986,7 @@ GroupCorrelation <- function(
   grp.cors <- as.data.frame(x = grp.cors[which(x = !is.na(x = grp.cors))])
   grp.cors$gene_grp <- gene.grp[rownames(x = grp.cors)]
   colnames(x = grp.cors) <- c(paste0(var, "_cor"), "feature.grp")
-  object[[assay]][] <- grp.cors
+  object[[assay]] <- AddMetaData(object[[assay]], grp.cors)
   if (isTRUE(x = do.plot)) {
     print(GroupCorrelationPlot(
       object = object,

R/visualization.R

@@ -4700,7 +4700,7 @@ GroupCorrelationPlot <- function(
   cor = "nCount_RNA_cor"
 ) {
   assay <- assay %||% DefaultAssay(object = object)
-  data <- object[[assay]][c(feature.group, cor)]
+  data <- object[[assay]][[c(feature.group, cor)]]
   data <- data[complete.cases(data), ]
   colnames(x = data) <- c('grp', 'cor')
   data$grp <- as.character(data$grp)