as_tibble() and slice_sample() cannot handle a column named $cell

[ttriche]

If you're dying to reproduce the whole thing, see https://github.com/VanAndelInstitute/ExpDesign2021/blob/main/vignettes/project2.md for gory details.

The bug:

R> as_tibble(tidybarnyard) %>% filter(method == "inDrops") %>% slice_sample()
Error: Can't transform a data frame with duplicate names.
Run `rlang::last_error()` to see where the error occurred.

Currently the fix is to rename that column. But that's a crappy fix!

R> names(colData(tidybarnyard))[4] <- "barcode"
R> as_tibble(tidybarnyard) %>% filter(method == "inDrops") %>% slice_sample()
# A tibble: 1 × 5
  cell                                        name    experiment method  barcode
  <chr>                                       <chr>   <chr>      <chr>   <chr>  
1 Mixture2.inDrops.ACCACAGA-AAGAGCGT-CTTGGTGT Mixtur… Mixture2   inDrops ACCACA…

Session info:

R> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 21.04

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.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       

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

other attached packages:
 [1] forcats_0.5.1                  readr_2.1.0                   
 [3] tidyverse_1.3.1                stringr_1.4.0                 
 [5] RcppML_0.5.2                   tidySingleCellExperiment_1.4.0
 [7] SingleCellExperiment_1.16.0    SummarizedExperiment_1.24.0   
 [9] Biobase_2.54.0                 GenomicRanges_1.46.0          
[11] GenomeInfoDb_1.30.0            IRanges_2.28.0                
[13] S4Vectors_0.32.2               BiocGenerics_0.40.0           
[15] MatrixGenerics_1.6.0           matrixStats_0.61.0            
[17] nvimcom_0.9-122                colorout_1.2-2                
[19] skeletor_1.0.4                 gtools_3.9.2                  
[21] useful_1.2.6                   knitr_1.36                    
[23] yardstick_0.0.8                workflowsets_0.1.0            
[25] workflows_0.2.4                tune_0.1.6                    
[27] tidyr_1.1.4                    tibble_3.1.6                  
[29] rsample_0.1.1                  recipes_0.1.17                
[31] purrr_0.3.4                    parsnip_0.1.7.9001            
[33] modeldata_0.1.1                infer_1.0.0                   
[35] ggplot2_3.3.5                  dplyr_1.0.7                   
[37] dials_0.0.10                   scales_1.1.1                  
[39] broom_0.7.10                   tidymodels_0.1.4              
[41] BiocManager_1.30.16           

loaded via a namespace (and not attached):
  [1] readxl_1.3.1           backports_1.3.0        RcppEigen_0.3.3.9.1   
  [4] plyr_1.8.6             lazyeval_0.2.2         splines_4.1.1         
  [7] listenv_0.8.0          usethis_2.1.3          digest_0.6.28         
 [10] foreach_1.5.1          htmltools_0.5.2        fansi_0.5.0           
 [13] magrittr_2.0.1         memoise_2.0.0.9000     tzdb_0.2.0            
 [16] remotes_2.4.1          globals_0.14.0         modelr_0.1.8          
 [19] gower_0.2.2            hardhat_0.1.6          prettyunits_1.1.1     
 [22] colorspace_2.0-2       rvest_1.0.2            haven_2.4.3           
 [25] xfun_0.28              tcltk_4.1.1            callr_3.7.0           
 [28] crayon_1.4.2           RCurl_1.98-1.5         jsonlite_1.7.2        
 [31] roxygen2_7.1.2         survival_3.2-13        iterators_1.0.13      
 [34] glue_1.5.0             gtable_0.3.0           ipred_0.9-12          
 [37] zlibbioc_1.40.0        XVector_0.34.0         DelayedArray_0.20.0   
 [40] pkgbuild_1.2.0         future.apply_1.8.1     DBI_1.1.1             
 [43] Rcpp_1.0.7             viridisLite_0.4.0      GPfit_1.0-8           
 [46] lava_1.6.10            prodlim_2019.11.13     htmlwidgets_1.5.4     
 [49] httr_1.4.2             ellipsis_0.3.2         pkgconfig_2.0.3       
 [52] nnet_7.3-16            dbplyr_2.1.1           utf8_1.2.2            
 [55] tidyselect_1.1.1       rlang_0.4.12           DiceDesign_1.9        
 [58] cellranger_1.1.0       munsell_0.5.0          tools_4.1.1           
 [61] cachem_1.0.6           cli_3.1.0              generics_0.1.1        
 [64] devtools_2.4.2         fastmap_1.1.0          processx_3.5.2        
 [67] fs_1.5.0               future_1.23.0          xml2_1.3.2            
 [70] compiler_4.1.1         rstudioapi_0.13        plotly_4.10.0         
 [73] testthat_3.1.0         reprex_2.0.1           lhs_1.1.3             
 [76] stringi_1.7.5          ps_1.6.0               desc_1.4.0            
 [79] lattice_0.20-45        Matrix_1.3-4           vctrs_0.3.8           
 [82] pillar_1.6.4           lifecycle_1.0.1        furrr_0.2.3           
 [85] data.table_1.14.2      bitops_1.0-7           R6_2.5.1              
 [88] KernSmooth_2.23-20     parallelly_1.28.1      sessioninfo_1.2.1     
 [91] codetools_0.2-18       MASS_7.3-54            assertthat_0.2.1      
 [94] pkgload_1.2.3          rprojroot_2.0.2        withr_2.4.2           
 [97] GenomeInfoDbData_1.2.7 hms_1.1.1              parallel_4.1.1        
[100] grid_4.1.1             rpart_4.1-15           timeDate_3043.102     
[103] class_7.3-19           pROC_1.18.0            lubridate_1.8.0   

[stemangiola]

Thanks, @ttriche for the issue.

the plan is for to use .cell column name instead of cell so as to not have such issues. However, like to tidySummarizedExperiment the backwards-compatible conversion is tricky and requires some work (hard at the end of the year). But I will start it soon.

[stemangiola]

Hello @ttriche now the default cell column is .cell, with the old one deprecated but back compatible.

Could you please install the relative branch (linked above) and try your workflow? (github action fails for missing igraph in the virtual machine)

Thanks

[stemangiola]

Hello @ttriche, any news by any chance?

[stemangiola]

I close for inactivity, feel free to comment on if still a problem.