AddMetaData with data.frame as metadata fills NAs instead of data

[jonasfreimuth]

When using AddMetaData to add metadata columns via a data.frame object, the resulting added columns contain only NAs instead of the actual data.

library("Seurat")

dims <- c(5, 6)
dim_names <- list(LETTERS[seq_len(dims[1])], letters[seq_len(dims[2])])

data <- `dimnames<-`(
  matrix(runif(dims[1] * dims[2]), nrow = dims[1], ncol = dims[2]),
  dim_names
)
meta_data <- data.frame(cell_type = as.character(seq_len(ncol(data))))

mini_so <- CreateSeuratObject(data)
mini_so_meta <- AddMetaData(mini_so, meta_data)

cat("\n\nmeta_data:\n")
print(meta_data)
cat("\n\nSeurat object metadata slot, should contain meta_data:\n")
print(mini_so_meta@meta.data)
cat("\n\nSession info:\n")
print(sessionInfo())

Excerpt output for ´mini_so_meta@meta.data`:

     orig.ident nCount_RNA nFeature_RNA cell_type
a SeuratProject   1.439934            5      <NA>
b SeuratProject   1.714582            5      <NA>
c SeuratProject   3.170943            5      <NA>
d SeuratProject   2.085310            5      <NA>
e SeuratProject   3.430311            5      <NA>
f SeuratProject   2.643897            5      <NA>

Full output:

The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, were retired in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
Attaching SeuratObject


meta_data:
  cell_type
1         1
2         2
3         3
4         4
5         5
6         6


Seurat object metadata slot, should contain meta_data:
     orig.ident nCount_RNA nFeature_RNA cell_type
a SeuratProject   2.442678            5      <NA>
b SeuratProject   2.598159            5      <NA>
c SeuratProject   2.018998            5      <NA>
d SeuratProject   2.494010            5      <NA>
e SeuratProject   3.467824            5      <NA>
f SeuratProject   1.654405            5      <NA>


Session info:
R version 4.3.1 (2023-06-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS/LAPACK: /gnu/store/d94sxy6axgzd3xr6bnp49l4v1nqzf825-openblas-0.3.20/lib/libopenblasp-r0.3.20.so;  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: Europe/Berlin
tzcode source: system (glibc)

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

other attached packages:
[1] SeuratObject_4.1.4 Seurat_4.4.0      

loaded via a namespace (and not attached):
  [1] deldir_1.0-9           pbapply_1.7-2          gridExtra_2.3         
  [4] rlang_1.1.1            magrittr_2.0.3         RcppAnnoy_0.0.21      
  [7] matrixStats_1.0.0      ggridges_0.5.4         compiler_4.3.1        
 [10] spatstat.geom_3.2-5    png_0.1-8              vctrs_0.6.3           
 [13] reshape2_1.4.4         stringr_1.5.0          pkgconfig_2.0.3       
 [16] fastmap_1.1.1          ellipsis_0.3.2         utf8_1.2.3            
 [19] promises_1.2.1         purrr_1.0.2            jsonlite_1.8.7        
 [22] goftest_1.2-3          later_1.3.1            spatstat.utils_3.0-3  
 [25] irlba_2.3.5.1          parallel_4.3.1         cluster_2.1.4         
 [28] R6_2.5.1               ica_1.0-3              stringi_1.7.12        
 [31] RColorBrewer_1.1-3     spatstat.data_3.0-1    reticulate_1.32.0     
 [34] parallelly_1.36.0      lmtest_0.9-40          scattermore_1.2       
 [37] Rcpp_1.0.11            tensor_1.5             future.apply_1.11.0   
 [40] zoo_1.8-12             sctransform_0.4.0      httpuv_1.6.11         
 [43] Matrix_1.6-1.1         splines_4.3.1          igraph_1.5.1          
 [46] tidyselect_1.2.0       abind_1.4-5            codetools_0.2-19      
 [49] spatstat.random_3.1-6  miniUI_0.1.1.1         spatstat.explore_3.2-3
 [52] listenv_0.9.0          lattice_0.21-9         tibble_3.2.1          
 [55] plyr_1.8.9             shiny_1.7.4            ROCR_1.0-11           
 [58] Rtsne_0.16             future_1.33.0          survival_3.5-7        
 [61] polyclip_1.10-6        fitdistrplus_1.1-11    pillar_1.9.0          
 [64] KernSmooth_2.23-22     plotly_4.10.2          generics_0.1.3        
 [67] sp_2.1-0               ggplot2_3.4.3          munsell_0.5.0         
 [70] scales_1.2.1           globals_0.16.2         xtable_1.8-4          
 [73] glue_1.6.2             lazyeval_0.2.2         tools_4.3.1           
 [76] data.table_1.14.8      RANN_2.6.1             leiden_0.4.3          
 [79] cowplot_1.1.1          grid_4.3.1             tidyr_1.3.0           
 [82] colorspace_2.1-0       nlme_3.1-163           patchwork_1.1.3       
 [85] cli_3.6.1              spatstat.sparse_3.0-2  fansi_1.0.5           
 [88] viridisLite_0.4.2      dplyr_1.1.3            uwot_0.1.16           
 [91] gtable_0.3.4           digest_0.6.33          progressr_0.14.0      
 [94] ggrepel_0.9.3          htmlwidgets_1.6.2      htmltools_0.5.6.1     
 [97] lifecycle_1.0.3        httr_1.4.7             mime_0.12             
[100] MASS_7.3-60