duplicate 'row.names' are not allowed

[stemangiola]

Hi @multimeric ,

I get this error for this query

  library(CuratedAtlasQueryR)  # For accessing curated atlas data
  library(tidyverse)          # For data manipulation and visualization
  
  # Retrieve and process the metadata
  get_metadata() |> 
    # Filter for specific conditions
    filter(
      tissue_harmonised == "blood",          # Select only 'blood' tissue
      cell_type_harmonised == "b memory",    # Select only 'b memory' cell type
      disease %in% c("normal", "COVID-19")   # Filter for 'normal' and 'COVID-19' diseases
    ) |> 
    # Convert the data frame to a tibble for better handling
    as_tibble() |> 
    # Nest data excluding sample and disease columns
    nest(data_cells = -c(sample_, disease)) |> 
    # Add a new column 'n' that contains the row count of each nested dataframe
    mutate(n = map_int(data_cells, nrow)) |> 
    # Filter out groups with less than 10 rows
    filter(n > 9) |> 
    # Nest the data again, this time excluding the disease column
    nest(data_samples = -disease) |> 
    # Add columns for lower and upper count thresholds
    mutate(count_low = c(10, 10), count_high = c(500, 10)) |> 
    # Apply function to each row using parallel mapping
    mutate(data_samples = pmap(
      list(data_samples, count_low, count_high),
      ~ bind_rows(
        # Select nine samples closest to the lower count threshold
        ..1 |> 
          arrange(abs(n-..2)) |> 
          head(9),
        
        # Select one sample closest to the higher count threshold
        ..1 |> 
          arrange(abs(n-..3)) |> 
          head(1)
      )
    )) |> 
    # Unnest the nested 'data_samples' dataframe
    unnest(data_samples) |> 
    # Group by 'disease' and sort each group by 'n'
    with_groups(disease, ~ .x |> arrange(n)) |> 
    # Finally, unnest the 'data_cells' to expand the nested data
    unnest(data_cells) |> 
    get_single_cell_experiment()

! Some cells were filtered out while loading 503aba0168fd5b11b6719b7cf61126bfbecause of extremely low counts. Thenumber of cells in the SingleCellExperiment will be less than thenumber of cells you have selected from the metadata.
Error in `map2()`:
ℹ In index: 1.
ℹ With name: counts.
Caused by error in `dplyr::summarise()`:
ℹ In argument: `sces = list(...)`.
ℹ In group 6: `file_id_db = "503aba0168fd5b11b6719b7cf61126bf"`.
Caused by error in `.rowNamesDF<-`:
! duplicate 'row.names' are not allowed
Run `rlang::last_trace()` to see where the error occurred.
Warning message:
In .f(.x[[i]], ...) : NAs introduced by coercion to integer range
> rlang::last_trace()
<error/purrr_error_indexed>
Error in `map2()`:
ℹ In index: 1.
ℹ With name: counts.
Caused by error in `dplyr::summarise()`:
ℹ In argument: `sces = list(...)`.
ℹ In group 6: `file_id_db = "503aba0168fd5b11b6719b7cf61126bf"`.
Caused by error in `.rowNamesDF<-`:
! duplicate 'row.names' are not allowed
---
Backtrace:
     ▆
  1. ├─CuratedAtlasQueryR::get_single_cell_experiment(...)
  2. │ └─purrr::imap(...)
  3. │   └─purrr::map2(.x, vec_index(.x), .f, ...)
  4. │     └─purrr:::map2_("list", .x, .y, .f, ..., .progress = .progress)
  5. │       ├─purrr:::with_indexed_errors(...)
  6. │       │ └─base::withCallingHandlers(...)
  7. │       ├─purrr:::call_with_cleanup(...)
  8. │       └─CuratedAtlasQueryR (local) .f(.x[[i]], .y[[i]], ...)
  9. │         ├─base::do.call(...)
 10. │         ├─dplyr::pull(...)
 11. │         ├─dplyr::summarise(...)
 12. │         └─dplyr:::summarise.grouped_df(...)
 13. │           └─dplyr:::summarise_cols(.data, dplyr_quosures(...), by, "summarise")
 14. │             ├─base::withCallingHandlers(...)
 15. │             └─dplyr:::map(quosures, summarise_eval_one, mask = mask)
 16. │               └─base::lapply(.x, .f, ...)
 17. │                 └─dplyr (local) FUN(X[[i]], ...)
 18. │                   └─mask$eval_all_summarise(quo)
 19. │                     └─dplyr (local) eval()
 20. └─CuratedAtlasQueryR:::group_to_sce(...)
 21.   ├─methods::as(...)
 22.   │ └─methods:::.class1(object)
 23.   └─tibble::column_to_rownames(...)
 24.     └─base::`rownames<-`(`*tmp*`, value = .data[[var]])
 25.       ├─base::`row.names<-`(`*tmp*`, value = value)
 26.       └─base::`row.names<-.data.frame`(`*tmp*`, value = value)
 27.         └─base::`.rowNamesDF<-`(x, value = value)
 28.           └─base::stop("duplicate 'row.names' are not allowed")

> sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /stornext/System/data/apps/R/R-4.3.0/lib64/R/lib/libRblas.so 
LAPACK: /stornext/System/data/apps/R/R-4.3.0/lib64/R/lib/libRlapack.so;  LAPACK version 3.11.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: UTC
tzcode source: system (glibc)

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

other attached packages:
 [1] lubridate_1.9.3          forcats_1.0.0            stringr_1.5.1            dplyr_1.1.4             
 [5] purrr_1.0.2              readr_2.1.4              tidyr_1.3.0              tibble_3.2.1            
 [9] ggplot2_3.4.4            tidyverse_2.0.0          CuratedAtlasQueryR_1.1.1

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.21            splines_4.3.0               later_1.3.1                
  [4] bitops_1.0-7                polyclip_1.10-6             fastDummies_1.7.3          
  [7] lifecycle_1.0.4             StanHeaders_2.33.1.9000     globals_0.16.2             
 [10] processx_3.8.2              lattice_0.22-5              MASS_7.3-60                
 [13] magrittr_2.0.3              plotly_4.10.3               httpuv_1.6.12              
 [16] Seurat_5.0.1                sctransform_0.4.1           spam_2.10-0                
 [19] sp_2.1-2                    pkgbuild_1.4.2              spatstat.sparse_3.0-3      
 [22] reticulate_1.34.0           cowplot_1.1.1               pbapply_1.7-2              
 [25] DBI_1.1.3                   minqa_1.2.6                 RColorBrewer_1.1-3         
 [28] abind_1.4-5                 zlibbioc_1.48.0             GenomicRanges_1.54.1       
 [31] Rtsne_0.16                  RCurl_1.98-1.12             BiocGenerics_0.48.1        
 [34] GenomeInfoDbData_1.2.11     IRanges_2.36.0              S4Vectors_0.40.2           
 [37] ggrepel_0.9.4               inline_0.3.19               irlba_2.3.5.1              
 [40] listenv_0.9.0               spatstat.utils_3.0-4        goftest_1.2-3              
 [43] RSpectra_0.16-1             spatstat.random_3.2-2       fitdistrplus_1.1-11        
 [46] parallelly_1.36.0           leiden_0.4.3.1              codetools_0.2-19           
 [49] DelayedArray_0.28.0         tidyselect_1.2.0            farver_2.1.1               
 [52] lme4_1.1-35.1               matrixStats_1.2.0           stats4_4.3.0               
 [55] spatstat.explore_3.2-5      duckdb_0.9.2-1              jsonlite_1.8.8             
 [58] ellipsis_0.3.2              progressr_0.14.0            ggridges_0.5.4             
 [61] survival_3.5-7              tools_4.3.0                 ica_1.0-3                  
 [64] Rcpp_1.0.11                 glue_1.6.2                  gridExtra_2.3              
 [67] SparseArray_1.2.2           MatrixGenerics_1.14.0       GenomeInfoDb_1.38.2        
 [70] HDF5Array_1.30.0            withr_2.5.2                 loo_2.6.0                  
 [73] numDeriv_2016.8-1.1         fastmap_1.1.1               boot_1.3-28.1              
 [76] rhdf5filters_1.14.0         fansi_1.0.5                 callr_3.7.3                
 [79] digest_0.6.33               timechange_0.2.0            R6_2.5.1                   
 [82] mime_0.12                   colorspace_2.1-0            scattermore_1.2            
 [85] tensor_1.5                  spatstat.data_3.0-3         utf8_1.2.4                 
 [88] generics_0.1.3              data.table_1.14.8           prettyunits_1.2.0          
 [91] httr_1.4.7                  htmlwidgets_1.6.3           S4Arrays_1.2.0             
 [94] uwot_0.1.16                 pkgconfig_2.0.3             gtable_0.3.4               
 [97] blob_1.2.4                  lmtest_0.9-40               SingleCellExperiment_1.24.0
[100] XVector_0.42.0              htmltools_0.5.7             dotCall64_1.1-1            
[103] Biobase_2.62.0              SeuratObject_5.0.1          scales_1.3.0               
[106] png_0.1-8                   nanonext_0.11.0             rstudioapi_0.15.0          
[109] tzdb_0.4.0                  reshape2_1.4.4              nlme_3.1-164               
[112] curl_5.2.0                  nloptr_2.0.3                crew_0.7.0                 
[115] zoo_1.8-12                  rhdf5_2.46.0                KernSmooth_2.23-22         
[118] parallel_4.3.0              miniUI_0.1.1.1              pillar_1.9.0               
[121] grid_4.3.0                  vctrs_0.6.5                 RANN_2.6.1                 
[124] promises_1.2.1              dbplyr_2.4.0                xtable_1.8-4               
[127] cluster_2.1.6               cli_3.6.2                   compiler_4.3.0             
[130] rlang_1.1.2                 crayon_1.5.2                crew.cluster_0.1.4         
[133] future.apply_1.11.0         ps_1.7.5                    plyr_1.8.9                 
[136] stringi_1.8.2               rstan_2.32.3                viridisLite_0.4.2          
[139] deldir_2.0-2                QuickJSR_1.0.8              assertthat_0.2.1           
[142] getip_0.1-3                 lmerTest_3.1-3              munsell_0.5.0              
[145] lazyeval_0.2.2              spatstat.geom_3.2-7         V8_4.4.0                   
[148] Matrix_1.6-4                RcppHNSW_0.5.0              hms_1.1.3                  
[151] patchwork_1.1.3             future_1.33.0               Rhdf5lib_1.24.0            
[154] shiny_1.8.0                 SummarizedExperiment_1.32.0 ROCR_1.0-11                
[157] mirai_0.11.3                igraph_1.5.0.1              RcppParallel_5.1.7