BUG: Error: ! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.

[chichen24601]

Issue Description

Hi Seurat team,

I'm trying to run BANKSY on a 10x Visium HD dataset (binned at 8µm, assay named "Spatial.008um") using SeuratWrappers::RunBanksy() as part of the Seurat Visium HD analysis vignette, but it fails immediately with the following error that "Error:
! The slot argument of GetAssayData() was deprecated in SeuratObject 5.0.0 and is now defunct. "

Reproducing Code Example

> packageVersion("Seurat")
[1] ‘5.3.1.1000’
> packageVersion("SeuratObject")
[1] ‘5.3.0’

> object <- RunBanksy(object,
+                     lambda = 0.8, 
+                     verbose = TRUE,
+                     assay = "Spatial.008um", 
+                     slot = "data", 
+                     features = "variable",
+                     k_geom = 50
+ )

Fetching data from slot data from assay Spatial.008um
Error: 
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
ℹ Please use the `layer` argument instead.
Run `rlang::last_trace()` to see where the error occurred.

Error Message

Additional Comments

No response

Session Info

> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 17763)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

time zone: Asia/Tokyo
tzcode source: internal

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

other attached packages:
 [1] remotes_2.5.0        Banksy_1.5.10        SeuratWrappers_0.4.0 Matrix_1.7-0         sf_1.0-23            dplyr_1.1.4         
 [7] patchwork_1.3.2      ggplot2_4.0.1        Seurat_5.3.1.1000    SeuratObject_5.3.0   sp_2.2-0            

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3          rstudioapi_0.17.1           jsonlite_2.0.0              magrittr_2.0.4             
  [5] magick_2.9.0                spatstat.utils_3.2-0        farver_2.1.2                zlibbioc_1.52.0            
  [9] vctrs_0.6.5                 ROCR_1.0-11                 spatstat.explore_3.6-0      S4Arrays_1.6.0             
 [13] htmltools_0.5.9             SparseArray_1.6.2           sctransform_0.4.2           parallelly_1.46.0          
 [17] KernSmooth_2.23-22          htmlwidgets_1.6.4           ica_1.0-3                   plyr_1.8.9                 
 [21] plotly_4.11.0               zoo_1.8-14                  igraph_2.2.1                mime_0.13                  
 [25] lifecycle_1.0.4             pkgconfig_2.0.3             rsvd_1.0.5                  R6_2.6.1                   
 [29] fastmap_1.2.0               aricode_1.0.3               GenomeInfoDbData_1.2.13     MatrixGenerics_1.18.1      
 [33] fitdistrplus_1.2-4          future_1.68.0               shiny_1.12.1                digest_0.6.39              
 [37] S4Vectors_0.44.0            tensor_1.5.1                RSpectra_0.16-2             irlba_2.3.5.1              
 [41] GenomicRanges_1.58.0        sccore_1.0.6                progressr_0.18.0            spatstat.sparse_3.1-0      
 [45] httr_1.4.7                  polyclip_1.10-7             abind_1.4-8                 compiler_4.4.0             
 [49] proxy_0.4-28                withr_3.0.2                 S7_0.2.1                    DBI_1.2.3                  
 [53] fastDummies_1.7.5           R.utils_2.13.0              MASS_7.3-60.2               DelayedArray_0.32.0        
 [57] rjson_0.2.23                classInt_0.4-11             tools_4.4.0                 units_1.0-0                
 [61] lmtest_0.9-40               otel_0.2.0                  httpuv_1.6.16               future.apply_1.20.1        
 [65] goftest_1.2-3               R.oo_1.27.1                 glue_1.8.0                  dbscan_1.2.3               
 [69] nlme_3.1-164                promises_1.5.0              grid_4.4.0                  Rtsne_0.17                 
 [73] cluster_2.1.6               reshape2_1.4.5              generics_0.1.4              gtable_0.3.6               
 [77] spatstat.data_3.1-9         R.methodsS3_1.8.2           class_7.3-22                tidyr_1.3.1                
 [81] data.table_1.17.8           XVector_0.46.0              BiocGenerics_0.52.0         spatstat.geom_3.6-1        
 [85] RcppAnnoy_0.0.22            ggrepel_0.9.6               RANN_2.6.2                  pillar_1.11.1              
 [89] stringr_1.6.0               spam_2.11-1                 RcppHNSW_0.6.0              RcppHungarian_0.3          
 [93] later_1.4.4                 splines_4.4.0               lattice_0.22-6              survival_3.5-8             
 [97] deldir_2.0-4                tidyselect_1.2.1            SingleCellExperiment_1.28.1 miniUI_0.1.2               
[101] pbapply_1.7-4               gridExtra_2.3               IRanges_2.40.1              SummarizedExperiment_1.36.0
[105] scattermore_1.2             stats4_4.4.0                Biobase_2.66.0              matrixStats_1.5.0          
[109] UCSC.utils_1.2.0            stringi_1.8.7               lazyeval_0.2.2              codetools_0.2-20           
[113] tibble_3.3.0                BiocManager_1.30.27         cli_3.6.5                   uwot_0.2.4                 
[117] leidenAlg_1.1.5             xtable_1.8-4                reticulate_1.44.1           GenomeInfoDb_1.42.3        
[121] Rcpp_1.1.0                  globals_0.18.0              spatstat.random_3.4-3       png_0.1-8                  
[125] spatstat.univar_3.1-5       parallel_4.4.0              mclust_6.1.2                dotCall64_1.2              
[129] SpatialExperiment_1.16.0    listenv_0.10.0              viridisLite_0.4.2           scales_1.4.0               
[133] ggridges_0.5.7              e1071_1.7-16                crayon_1.5.3                purrr_1.2.0

[anashen]

Hi @chichen24601,

Thanks for the report -- the calls to GetAssayData and SetAssayData in RunBanksy (from SeuratWrappers) still use the slot parameter (had been deprecated in SeuratObject v5.0.0 since Oct 2023, now defunct).

We will fix this very soon in SeuratWrappers; a quick fix until then would be to downgrade SeuratObject.

[anashen]

Hi @chichen24601,

This has now been fixed via satijalab/seurat-wrappers#223. Please install the latest version of SeuratWrappers, and be sure to restart your R session afterwards.

remotes::install_github("satijalab/seurat-wrappers", force = TRUE)

[ssukumaran2]

Hi,
I am having the same issue with RunALRA command. Sueratwrappers was updated and R was restarted, but the issue is not resolved. I am using seurat 5.4.0.

CVMoFacs<-RunALRA(CVMoFacs, layer='data')
Error:
! The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is
  now defunct.
ℹ Please use the `layer` argument instead.
Run `rlang::last_trace()` to see where the error occurred.

> packageVersion("SeuratObject")
[1] ‘5.3.0’
> packageVersion("Seurat")
[1] ‘5.4.0’

[anashen]

Updating the issue for others to add that RunALRA is also fixed; see satijalab/seurat-wrappers#225.

---

Note

Make sure to use layer instead of slot in calls to GetAssayData, SetAssayData, etc. to avoid the error in your packages / workflows that use Seurat. (Params / functions deprecated in SeuratObject v5.0.0 (Oct 2023) had been scheduled for eventual defunction after 3 releases.) If there are problematic calls in SeuratWrappers, please open a new issue and we will work to fix it ASAP. Thank you!

[chichen24601]

RunBanksy() now works. Thank you very much!