CreateSeuratObject fails when counts is a matrix

[lazappi]

I'm getting the following error when I try to create a Seurat object from a matrix. A data frame seems to work fine so not sure exactly what is going on.

library(SeuratObject)

pbmc_raw <- read.table(
    file = system.file('extdata', 'pbmc_raw.txt', package = 'Seurat'),
    as.is = TRUE
)

CreateSeuratObject(counts = pbmc_raw)
#> An object of class Seurat 
#> 230 features across 80 samples within 1 assay 
#> Active assay: RNA (230 features, 0 variable features)

CreateSeuratObject(counts = as.matrix(pbmc_raw))
#> Error in switch(EXPR = getOption(x = "Seurat.checkdots"), warn = warning(msg, : EXPR must be a length 1 vector

^{Created on 2021-05-13 by the reprex package (v2.0.0)}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                                             
#>  version  R Under development (unstable) (2021-03-29 r80130)
#>  os       macOS Catalina 10.15.7                            
#>  system   x86_64, darwin17.0                                
#>  ui       X11                                               
#>  language (EN)                                              
#>  collate  en_US.UTF-8                                       
#>  ctype    en_US.UTF-8                                       
#>  tz       Europe/Berlin                                     
#>  date     2021-05-13                                        
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package      * version date       lib source             
#>  backports      1.2.1   2020-12-09 [1] standard (@1.2.1)  
#>  cli            2.5.0   2021-04-26 [1] standard (@2.5.0)  
#>  crayon         1.4.1   2021-02-08 [1] CRAN (R 4.1.0)     
#>  digest         0.6.27  2020-10-24 [1] CRAN (R 4.1.0)     
#>  ellipsis       0.3.2   2021-04-29 [1] CRAN (R 4.1.0)     
#>  evaluate       0.14    2019-05-28 [1] standard (@0.14)   
#>  fansi          0.4.2   2021-01-15 [1] CRAN (R 4.1.0)     
#>  fs             1.5.0   2020-07-31 [1] standard (@1.5.0)  
#>  glue           1.4.2   2020-08-27 [1] CRAN (R 4.1.0)     
#>  highr          0.9     2021-04-16 [1] standard (@0.9)    
#>  htmltools      0.5.1.1 2021-01-22 [1] standard (@0.5.1.1)
#>  knitr          1.33    2021-04-24 [1] standard (@1.33)   
#>  lattice        0.20-44 2021-05-02 [1] CRAN (R 4.1.0)     
#>  lifecycle      1.0.0   2021-02-15 [1] CRAN (R 4.1.0)     
#>  magrittr       2.0.1   2020-11-17 [1] CRAN (R 4.1.0)     
#>  Matrix         1.3-3   2021-05-04 [1] CRAN (R 4.1.0)     
#>  pillar         1.6.0   2021-04-13 [1] CRAN (R 4.1.0)     
#>  pkgconfig      2.0.3   2019-09-22 [1] CRAN (R 4.1.0)     
#>  purrr          0.3.4   2020-04-17 [1] standard (@0.3.4)  
#>  Rcpp           1.0.6   2021-01-15 [1] standard (@1.0.6)  
#>  reprex         2.0.0   2021-04-02 [1] standard (@2.0.0)  
#>  rlang          0.4.11  2021-04-30 [1] CRAN (R 4.1.0)     
#>  rmarkdown      2.8     2021-05-07 [1] CRAN (R 4.1.0)     
#>  sessioninfo    1.1.1   2018-11-05 [1] standard (@1.1.1)  
#>  SeuratObject * 4.0.1   2021-05-08 [1] standard (@4.0.1)  
#>  stringi        1.6.1   2021-05-10 [1] CRAN (R 4.1.0)     
#>  stringr        1.4.0   2019-02-10 [1] CRAN (R 4.1.0)     
#>  styler         1.4.1   2021-03-30 [1] standard (@1.4.1)  
#>  tibble         3.1.1   2021-04-18 [1] CRAN (R 4.1.0)     
#>  utf8           1.2.1   2021-03-12 [1] CRAN (R 4.1.0)     
#>  vctrs          0.3.8   2021-04-29 [1] CRAN (R 4.1.0)     
#>  withr          2.4.2   2021-04-18 [1] CRAN (R 4.1.0)     
#>  xfun           0.22    2021-03-11 [1] standard (@0.22)   
#>  yaml           2.2.1   2020-02-01 [1] standard (@2.2.1)  
#> 
#> [1] /Library/Frameworks/R.framework/Versions/4.1/Resources/library

[lazappi]

This works if you do library(Seurat) first, so I'm guessing that is setting something? Maybe SeuratObject needs to do the same?

[mojaveazure]

Hi Luke, thanks for bringing this up. Can you try with the a patch on the fix/checkdots branch?

if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
remotes::install_github("mojaveazure/seurat-object", ref = "fix/checkdots")

[lazappi]

That seems to work! 🎉

Just in case it's interesting I got this error on R 4.1. Not sure if it is something to do with SeuratObject or remotes

> remotes::install_github("mojaveazure/seurat-object", ref = "fix/checkdots")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo mojaveazure/seurat-object@fix/checkdots
Error: Failed to install 'SeuratObject' from GitHub:
  invalid 'type'

Worked ok on R 4.0 though.

[mojaveazure]

Sorry for the delay. Neither Andrew nor I have been able to replicate the installation issue. We think it's an issue with {remotes} instead of SeuratObject