merge SFE objects

[cathalgking]

I would like to merge 2 SFE objects however I am getting an error related to column(s) 'Feature.Type'. Is there a way to get past this?

I try with:

# load data
vis1 <- SpatialFeatureExperiment::read10xVisiumSFE(dirs = "../data/PTCVIS1/PTCVIS1/",
                                                   row.names = "symbol",
                                                   zero.policy = T)

vis1

#colnames(vis1) <- paste0("vis1_", colnames(vis1))

# load data
vis2 <- SpatialFeatureExperiment::read10xVisiumSFE(dirs = "../data/PTCVIS2/PTCVIS2/",
                                                   row.names = "symbol",
                                                   zero.policy = T)

vis2

vis_merged <- SpatialFeatureExperiment::cbind(vis1, vis2, deparse.level = 1)

'sample_id's are duplicated across 'SpatialFeatureExperiment' objects to cbind; appending sample indices.
Error in FUN(X[[i]], ...) : 
  column(s) 'Feature.Type' in ‘mcols’ are duplicated and the data do not match

> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS 15.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: Australia/Adelaide
tzcode source: internal

attached base packages:
[1] grid      stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] png_0.1-8                      SEtools_1.20.0                 sechm_1.14.0                   ComplexHeatmap_2.22.0          Seurat_5.1.0                  
 [6] SeuratObject_5.0.2             sp_2.1-4                       ggspavis_1.12.0                reticulate_1.42.0              BiocNeighbors_2.0.1           
[11] BiocParallel_1.40.2            dplyr_1.1.4                    sf_1.0-21                      rlang_1.1.6                    terra_1.8-50                  
[16] EBImage_4.48.0                 rjson_0.2.23                   bluster_1.16.0                 patchwork_1.3.0                stringr_1.5.1                 
[21] scran_1.34.0                   scater_1.34.1                  scuttle_1.16.0                 ggplot2_3.5.2                  SingleCellExperiment_1.28.1   
[26] SummarizedExperiment_1.36.0    Biobase_2.66.0                 GenomicRanges_1.58.0           GenomeInfoDb_1.42.3            IRanges_2.40.1                
[31] S4Vectors_0.44.0               BiocGenerics_0.52.0            MatrixGenerics_1.18.1          matrixStats_1.4.1              Voyager_1.8.1                 
[36] SpatialFeatureExperiment_1.8.6

loaded via a namespace (and not attached):
  [1] randomcoloR_1.1.0.1       SpatialExperiment_1.16.0  R.methodsS3_1.8.2         dichromat_2.0-0.1         tiff_0.1-12               goftest_1.2-3            
  [7] Biostrings_2.74.1         HDF5Array_1.34.0          TH.data_1.1-3             vctrs_0.6.5               spatstat.random_3.4-1     digest_0.6.37            
 [13] shape_1.4.6.1             proxy_0.4-27              registry_0.5-1            ggrepel_0.9.6             deldir_2.0-4              parallelly_1.44.0        
 [19] magick_2.8.6              MASS_7.3-65               reshape2_1.4.4            httpuv_1.6.15             foreach_1.5.2             scico_1.5.0              
 [25] withr_3.0.2               xfun_0.52                 survival_3.8-3            memoise_2.0.1             s2_1.1.9                  ggbeeswarm_0.7.2         
 [31] zoo_1.8-12                GlobalOptions_0.1.2       V8_6.0.3                  pbapply_1.7-2             R.oo_1.27.1               spData_2.3.4             
 [37] KEGGREST_1.46.0           promises_1.3.2            httr_1.4.7                globals_0.18.0            fitdistrplus_1.2-2        rhdf5filters_1.18.1      
 [43] rhdf5_2.50.2              rstudioapi_0.17.1         spatialreg_1.3-6          UCSC.utils_1.2.0          units_0.8-7               miniUI_0.1.1.1           
 [49] generics_0.1.4            curl_6.2.3                zlibbioc_1.52.0           ScaledMatrix_1.14.0       polyclip_1.10-7           ca_0.71.1                
 [55] GenomeInfoDbData_1.2.13   SparseArray_1.6.2         fftwtools_0.9-11          xtable_1.8-4              doParallel_1.0.17         evaluate_1.0.3           
 [61] S4Arrays_1.6.0            irlba_2.3.5.1             colorspace_2.1-1          hdf5r_1.3.12              ROCR_1.0-11               spatstat.data_3.1-6      
 [67] magrittr_2.0.3            lmtest_0.9-40             spdep_1.3-11              later_1.3.2               viridis_0.6.5             lattice_0.22-6           
 [73] spatstat.geom_3.4-1       future.apply_1.11.3       genefilter_1.88.0         scattermore_1.2           XML_3.99-0.17             cowplot_1.1.3            
 [79] RcppAnnoy_0.0.22          class_7.3-22              pillar_1.10.2             nlme_3.1-168              iterators_1.0.14          compiler_4.4.0           
 [85] beachmat_2.22.0           RSpectra_0.16-2           stringi_1.8.4             TSP_1.2-4                 tensor_1.5                plyr_1.8.9               
 [91] crayon_1.5.3              abind_1.4-8               locfit_1.5-9.12           bit_4.6.0                 sandwich_3.1-1            codetools_0.2-20         
 [97] multcomp_1.4-28           BiocSingular_1.22.0       e1071_1.7-16              GetoptLong_1.0.5          plotly_4.10.4             mime_0.13                
[103] splines_4.4.0             circlize_0.4.16           Rcpp_1.0.14               fastDummies_1.7.5         sparseMatrixStats_1.18.0  blob_1.2.4               
[109] knitr_1.50                clue_0.3-66               listenv_0.9.1             DelayedMatrixStats_1.28.1 openxlsx_4.2.8            tibble_3.2.1             
[115] Matrix_1.7-3              statmod_1.5.0             pkgconfig_2.0.3           pheatmap_1.0.12           tools_4.4.0               cachem_1.1.0             
[121] RSQLite_2.3.7             viridisLite_0.4.2         DBI_1.2.3                 fastmap_1.2.0             rmarkdown_2.29            scales_1.4.0             
[127] ica_1.0-3                 coda_0.19-4.1             BiocManager_1.30.25       dotCall64_1.2             LearnBayes_2.15.1         RANN_2.6.2               
[133] farver_2.1.2              mgcv_1.9-1                wk_0.9.4                  yaml_2.3.10               cli_3.6.5                 purrr_1.0.4              
[139] leiden_0.4.3.1            lifecycle_1.0.4           dbscan_1.2.2              rsconnect_1.4.1           uwot_0.2.2                mvtnorm_1.3-3            
[145] DropletUtils_1.26.0       annotate_1.84.0           gtable_0.3.6              ggridges_0.5.6            progressr_0.15.1          parallel_4.4.0           
[151] limma_3.62.2              jsonlite_2.0.0            edgeR_4.4.2               RcppHNSW_0.6.0            seriation_1.5.6           bitops_1.0-9             
[157] bit64_4.6.0-1             Rtsne_0.17                spatstat.utils_3.1-4      zip_2.3.1                 ggside_0.3.1              metapod_1.14.0           
[163] dqrng_0.4.1               zeallot_0.1.0             spatstat.univar_3.1-3     R.utils_2.13.0            lazyeval_0.2.2            shiny_1.10.0             
[169] htmltools_0.5.8.1         sctransform_0.4.1         glue_1.8.0                spam_2.11-1               XVector_0.46.0            RCurl_1.98-1.17          
[175] classInt_0.4-11           jpeg_0.1-11               gridExtra_2.3             boot_1.3-31               igraph_2.1.4              R6_2.6.1                 
[181] sva_3.54.0                tidyr_1.3.1               DESeq2_1.46.0             labeling_0.4.3            cluster_2.1.6             pkgload_1.4.0            
[187] Rhdf5lib_1.28.0           memuse_4.2-3              DelayedArray_0.32.0       tidyselect_1.2.1          vipor_0.4.7               AnnotationDbi_1.68.0     
[193] future_1.49.0             sfheaders_0.4.4           rsvd_1.0.5                KernSmooth_2.23-24        data.table_1.17.4         htmlwidgets_1.6.4        
[199] RColorBrewer_1.1-3        spatstat.sparse_3.1-0     spatstat.explore_3.4-3    ggnewscale_0.5.1          beeswarm_0.4.0     

@lambdamoses

[lambdamoses]

Sorry for the late response. I've been really busy preparing for a conference presentation. I think the cause of this error is that the contents of rowData of the two SFE objects don't match, here specifically the Feature.Type column in rowData, and the underlying SingleCellExperiment method doesn't know how to deal with that, because the combined object can only have one rowData. Can you check rowData(vis1) and rowData(vis2)?

[lambdamoses]

I think the culprit is spatial_enrichment.csv which is added to rowData if the file is present, and it might not match across different samples. I'll add an argument to read10xVisiumSFE() to indicate whether to read spatial_enrichment.csv. A way to get around your problem is

vis <- read10xVisiumSFE(dirs = c("../data/PTCVIS1/PTCVIS1/", "../data/PTCVIS2/PTCVIS2/"), 
row.names = "symbol",
zero.policy = T)

When you have spatial_enrichment.csv, the sample_id will be appended to its columns when you read both samples at ones line in the example here to avoid the conflict and cbind is performed internally.