BUG: AggregateExpression creates wrong metadata if a column in group.by has only one value.

[dimitrios-pm]

Issue Description

The AggregateExpression function behaves unexpectedly when passing arguments with only one value.
pseudo_data<- AggregateExpression(ifnb, assays = "RNA", return.seurat = TRUE, group.by = c("orig.ident","GROUP", "seurat_annotations"))
Which gives:
"The following grouping variables have 1 value and will be ignored: GROUP"
It creates a seurat object but that objects metadata are wrong.

I would expect the correct behaviour to be that if it would be ignored then the resulting object should have identical metadata as if that value is not there.

Reproducing Code Example

library(Seurat)
library(SeuratData)

ifnb <- LoadData("ifnb")

ifnb$GROUP <- "group1"
pseudo_data<- AggregateExpression(ifnb, assays = "RNA", return.seurat = TRUE, group.by = c("orig.ident", "seurat_annotations"))
pseudo_data2<- AggregateExpression(ifnb, assays = "RNA", return.seurat = TRUE, group.by = c("orig.ident","GROUP", "seurat_annotations"))

Error Message

Additional Comments

No response

Session Info

> sessionInfo()
R version 4.4.3 (2025-02-28 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_Denmark.utf8  LC_CTYPE=English_Denmark.utf8   
[3] LC_MONETARY=English_Denmark.utf8 LC_NUMERIC=C                    
[5] LC_TIME=English_Denmark.utf8    

time zone: Europe/Copenhagen
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods  
[7] base     

other attached packages:
[1] Seurat_5.2.1          SeuratObject_5.0.2    sp_2.2-0             
[4] ifnb.SeuratData_3.1.0 cbmc.SeuratData_3.1.4 SeuratData_0.2.2.9002

loaded via a namespace (and not attached):
  [1] deldir_2.0-4           pbapply_1.7-2         
  [3] gridExtra_2.3          remotes_2.5.0         
  [5] rlang_1.1.4            magrittr_2.0.3        
  [7] RcppAnnoy_0.0.22       spatstat.geom_3.3-5   
  [9] matrixStats_1.4.1      ggridges_0.5.6        
 [11] compiler_4.4.3         png_0.1-8             
 [13] callr_3.7.6            vctrs_0.6.5           
 [15] reshape2_1.4.4         stringr_1.5.1         
 [17] crayon_1.5.3           pkgconfig_2.0.3       
 [19] fastmap_1.2.0          promises_1.3.2        
 [21] ps_1.9.0               purrr_1.0.2           
 [23] jsonlite_1.8.8         goftest_1.2-3         
 [25] later_1.4.1            spatstat.utils_3.1-3  
 [27] irlba_2.3.5.1          parallel_4.4.3        
 [29] cluster_2.1.8          R6_2.6.1              
 [31] ica_1.0-3              stringi_1.8.4         
 [33] RColorBrewer_1.1-3     spatstat.data_3.1-6   
 [35] reticulate_1.41.0.1    parallelly_1.42.0     
 [37] spatstat.univar_3.1-2  lmtest_0.9-40         
 [39] scattermore_1.2        Rcpp_1.0.13-1         
 [41] tensor_1.5             future.apply_1.11.3   
 [43] zoo_1.8-13             sctransform_0.4.1     
 [45] httpuv_1.6.15          Matrix_1.7-2          
 [47] splines_4.4.3          igraph_2.1.3          
 [49] tidyselect_1.2.1       rstudioapi_0.17.1     
 [51] abind_1.4-8            spatstat.random_3.3-2 
 [53] codetools_0.2-20       miniUI_0.1.1.1        
 [55] spatstat.explore_3.3-4 curl_6.2.0            
 [57] processx_3.8.6         listenv_0.9.1         
 [59] pkgbuild_1.4.6         lattice_0.22-6        
 [61] tibble_3.2.1           plyr_1.8.9            
 [63] shiny_1.10.0           ROCR_1.0-11           
 [65] Rtsne_0.17             future_1.34.0         
 [67] fastDummies_1.7.5      desc_1.4.3            
 [69] survival_3.8-3         polyclip_1.10-7       
 [71] fitdistrplus_1.2-2     pillar_1.10.1         
 [73] KernSmooth_2.23-26     plotly_4.10.4         
 [75] generics_0.1.3         RcppHNSW_0.6.0        
 [77] ggplot2_3.5.1          munsell_0.5.1         
 [79] scales_1.3.0           globals_0.16.3        
 [81] xtable_1.8-4           glue_1.7.0            
 [83] lazyeval_0.2.2         tools_4.4.3           
 [85] data.table_1.15.4      RSpectra_0.16-2       
 [87] RANN_2.6.2             dotCall64_1.2         
 [89] cowplot_1.1.3          grid_4.4.3            
 [91] tidyr_1.3.1            colorspace_2.1-1      
 [93] nlme_3.1-167           patchwork_1.3.0       
 [95] cli_3.6.3              rappdirs_0.3.3        
 [97] spatstat.sparse_3.1-0  spam_2.11-1           
 [99] viridisLite_0.4.2      dplyr_1.1.4           
[101] uwot_0.2.3             gtable_0.3.6          
[103] digest_0.6.37          progressr_0.15.1      
[105] ggrepel_0.9.6          htmlwidgets_1.6.4     
[107] farver_2.1.2           htmltools_0.5.8.1     
[109] lifecycle_1.0.4        httr_1.4.7            
[111] mime_0.12              MASS_7.3-64