After integrate two object, and then split then, there are something wrong with Cells() function

[tangmindan]

Hi, when I try to split an object from an integrate object and then rename its cell names, I've got an error which hints the length difference between Cells(split_object) and rownames([email protected])

# insert reproducible example here
opt$input <- "object1.rData,object2.rData"
data <- unlist(strsplit(opt$input,","))
object_merge <- list()
for (i in 1:length(data)){
	load(data[i])
	object_merge[[i]] <- get("object") 
}
object_merged <- Reduce(function(x, y) merge(x, y), object_merge)
object <- object_merged
integrate_obj <- IntegrateLayers(object = object, method = "RPCAIntegration", orig.reduction = "pca", new.reduction = integrate_name,
    verbose = FALSE)
integrate_obj <- FindNeighbors(integrate_obj, reduction = integrate_name, dims = 1:20,nn.method = "rann")
integrate_obj <- FindClusters(integrate_obj, verbose = FALSE,resolution=res,algorithm = 1)
integrate_obj <- RunUMAP(integrate_obj, reduction = "integrated.RPCA", dims = 1:pca_dim,n.neighbors=15,min.dist=0.1)
object <- integrate_obj 
ifnb_list <- SplitObject(object, split.by = "orig.ident")
length(rownames(ifnb_list[[1]]@meta.data))
length(Cells(ifnb_list[[1]]))
cell_name <- substr(rownames(ifnb_list[[1]]@meta.data), 1, 21)
object <- RenameCells(ifnb_list[[1]], new.names=cell_name)
cell_name <- substr(Cells(ifnb_list[[1]]), 1, 21)
object <- RenameCells(ifnb_list[[1]], new.names=cell_name)

sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=zh_CN.utf8       LC_NUMERIC=C             
 [3] LC_TIME=zh_CN.utf8        LC_COLLATE=zh_CN.utf8    
 [5] LC_MONETARY=zh_CN.utf8    LC_MESSAGES=zh_CN.utf8   
 [7] LC_PAPER=zh_CN.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=zh_CN.utf8 LC_IDENTIFICATION=C      

time zone: Asia/Aden
tzcode source: system (glibc)

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

other attached packages:
 [1] RColorBrewer_1.1-3 tidyr_1.3.1        dplyr_1.1.4        glue_1.7.0        
 [5] patchwork_1.2.0    qs_0.26.3          ggplot2_3.5.1      Seurat_5.1.0      
 [9] SeuratObject_5.0.2 sp_2.1-4          

loaded via a namespace (and not attached):
  [1] deldir_2.0-4           pbapply_1.7-2          gridExtra_2.3         
  [4] rlang_1.1.4            magrittr_2.0.3         RcppAnnoy_0.0.22      
  [7] matrixStats_1.3.0      ggridges_0.5.6         compiler_4.4.0        
 [10] spatstat.geom_3.3-2    systemfonts_1.1.0      png_0.1-8             
 [13] vctrs_0.6.5            reshape2_1.4.4         stringr_1.5.1         
 [16] crayon_1.5.3           pkgconfig_2.0.3        fastmap_1.2.0         
 [19] labeling_0.4.3         utf8_1.2.4             promises_1.3.0        
 [22] ragg_1.3.2             purrr_1.0.2            jsonlite_1.8.8        
 [25] goftest_1.2-3          later_1.3.2            spatstat.utils_3.0-5  
 [28] irlba_2.3.5.1          parallel_4.4.0         cluster_2.1.6         
 [31] R6_2.5.1               ica_1.0-3              stringi_1.8.4         
 [34] spatstat.data_3.1-2    reticulate_1.38.0      parallelly_1.38.0     
 [37] spatstat.univar_3.0-0  lmtest_0.9-40          scattermore_1.2       
 [40] Rcpp_1.0.13            tensor_1.5             future.apply_1.11.2   
 [43] zoo_1.8-12             sctransform_0.4.1      httpuv_1.6.15         
 [46] Matrix_1.7-0           splines_4.4.0          igraph_2.0.3          
 [49] tidyselect_1.2.1       abind_1.4-5            stringfish_0.16.0     
 [52] spatstat.random_3.3-1  codetools_0.2-20       miniUI_0.1.1.1        
 [55] spatstat.explore_3.3-1 listenv_0.9.1          lattice_0.22-6        
 [58] tibble_3.2.1           plyr_1.8.9             withr_3.0.1           
 [61] shiny_1.9.1            ROCR_1.0-11            Rtsne_0.17            
 [64] future_1.34.0          fastDummies_1.7.3      survival_3.7-0        
 [67] RcppParallel_5.1.8     polyclip_1.10-7        fitdistrplus_1.2-1    
 [70] pillar_1.9.0           KernSmooth_2.23-24     plotly_4.10.4         
 [73] generics_0.1.3         RcppHNSW_0.6.0         munsell_0.5.1         
 [76] scales_1.3.0           RApiSerialize_0.1.3    globals_0.16.3        
 [79] xtable_1.8-4           lazyeval_0.2.2         tools_4.4.0           
 [82] data.table_1.15.4      RSpectra_0.16-2        RANN_2.6.1            
 [85] leiden_0.4.3.1         dotCall64_1.1-1        cowplot_1.1.3         
 [88] grid_4.4.0             colorspace_2.1-1       nlme_3.1-165          
 [91] cli_3.6.3              spatstat.sparse_3.1-0  textshaping_0.4.0     
 [94] spam_2.10-0            fansi_1.0.6            viridisLite_0.4.2     
 [97] uwot_0.2.2             gtable_0.3.5           digest_0.6.36         
[100] progressr_0.14.0       ggrepel_0.9.5          farver_2.1.2          
[103] htmlwidgets_1.6.4      htmltools_0.5.8.1      lifecycle_1.0.4       
[106] httr_1.4.7             mime_0.12              MASS_7.3-61