Seurat v5 Support

[shahrozeabbas]

Hi,

Love your package and hope to continue using it!

I believe SCpubr has support for Seuratv5 but I was having some trouble with the do_DimPlot function. Am I missing something?

> object <- readRDS('objects/merged.rds')
> p <- object %>% do_DimPlot(reduction='X_umap', group.by='leiden')
Loading required package: BPCells
Error in `asMethod()`:
! Error converting IterableMatrix to dgCMatrix
• dgCMatrix objects cannot hold more than 2^31 non-zero entries
• Input matrix has 3239391600 entries
Run `rlang::last_trace()` to see where the error occurred.
> sessionInfo()
R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Rocky Linux 8.7 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: /usr/local/intel/2022.1.2.146/mkl/2022.0.2/lib/intel64/libmkl_rt.so.2;  LAPACK version 3.9.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: America/New_York
tzcode source: system (glibc)

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

other attached packages:
[1] BPCells_0.2.0      dplyr_1.1.4        ggplot2_3.5.1      SCpubr_2.0.2      
[5] Seurat_5.1.0       SeuratObject_5.0.2 sp_2.1-4          

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3      jsonlite_1.8.8          magrittr_2.0.3         
  [4] spatstat.utils_3.0-5    zlibbioc_1.50.0         fs_1.6.4               
  [7] vctrs_0.6.5             ROCR_1.0-11             memoise_2.0.1          
 [10] spatstat.explore_3.2-7  htmltools_0.5.8.1       forcats_1.0.0          
 [13] gridGraphics_0.5-1      sctransform_0.4.1       parallelly_1.37.1      
 [16] KernSmooth_2.23-24      htmlwidgets_1.6.4       ica_1.0-3              
 [19] plyr_1.8.9              plotly_4.10.4           zoo_1.8-12             
 [22] cachem_1.1.0            igraph_2.0.3            mime_0.12              
 [25] lifecycle_1.0.4         pkgconfig_2.0.3         Matrix_1.7-0           
 [28] R6_2.5.1                fastmap_1.2.0           GenomeInfoDbData_1.2.12
 [31] MatrixGenerics_1.16.0   fitdistrplus_1.1-11     future_1.33.2          
 [34] shiny_1.8.1.1           digest_0.6.36           colorspace_2.1-0       
 [37] S4Vectors_0.42.0        patchwork_1.2.0         tensor_1.5             
 [40] RSpectra_0.16-1         irlba_2.3.5.1           GenomicRanges_1.56.1   
 [43] labeling_0.4.3          progressr_0.14.0        fansi_1.0.6            
 [46] spatstat.sparse_3.1-0   httr_1.4.7              polyclip_1.10-6        
 [49] abind_1.4-5             compiler_4.4.1          withr_3.0.0            
 [52] viridis_0.6.5           fastDummies_1.7.3       MASS_7.3-61            
 [55] tools_4.4.1             lmtest_0.9-40           httpuv_1.6.15          
 [58] future.apply_1.11.2     goftest_1.2-3           glue_1.7.0             
 [61] nlme_3.1-165            promises_1.3.0          grid_4.4.1             
 [64] Rtsne_0.17              cluster_2.1.6           reshape2_1.4.4         
 [67] generics_0.1.3          gtable_0.3.5            spatstat.data_3.1-2    
 [70] tidyr_1.3.1             data.table_1.15.4       XVector_0.44.0         
 [73] utf8_1.2.4              BiocGenerics_0.50.0     spatstat.geom_3.2-9    
 [76] RcppAnnoy_0.0.22        ggrepel_0.9.5           RANN_2.6.1             
 [79] pillar_1.9.0            stringr_1.5.1           yulab.utils_0.1.4      
 [82] spam_2.10-0             RcppHNSW_0.6.0          later_1.3.2            
 [85] splines_4.4.1           lattice_0.22-6          survival_3.7-0         
 [88] deldir_2.0-4            tidyselect_1.2.1        miniUI_0.1.1.1         
 [91] pbapply_1.7-2           gridExtra_2.3           IRanges_2.38.0         
 [94] scattermore_1.2         stats4_4.4.1            matrixStats_1.3.0      
 [97] UCSC.utils_1.0.0        stringi_1.8.4           lazyeval_0.2.2         
[100] codetools_0.2-20        tibble_3.2.1            ggplotify_0.1.2        
[103] cli_3.6.3               uwot_0.2.2              xtable_1.8-4           
[106] reticulate_1.38.0       munsell_0.5.1           GenomeInfoDb_1.40.1    
[109] Rcpp_1.0.12             globals_0.16.3          spatstat.random_3.2-3  
[112] png_0.1-8               parallel_4.4.1          assertthat_0.2.1       
[115] dotCall64_1.1-1         listenv_0.9.1           viridisLite_0.4.2      
[118] scales_1.3.0            ggridges_0.5.6          leiden_0.4.3.1         
[121] purrr_1.0.2             rlang_1.1.4             cowplot_1.1.3