merging VisiumHD objects fails due to RenameCells

[ddiez]

I am trying to merge 2 Seurat objects containing data loaded from VisiumHD technology:

> x1 <- RenameCells(x1, add.cell.id="B1")
> x2 <- RenameCells(x2, add.cell.id="B2")
> merge(x1, x2)
Warning: Some cell names are duplicated across objects provided. Renaming to enforce unique cell names.
Error in `RenameCells()`:
! the length of 'new.names' (492460) must be the same as the number of cells (98917)
Run `rlang::last_trace()` to see where the error occurred.
> head(colnames(x1))
[1] "B1_s_016um_00052_00082-1" "B1_s_016um_00150_00268-1"
[3] "B1_s_016um_00144_00175-1" "B1_s_016um_00165_00109-1"
[5] "B1_s_016um_00297_00147-1" "B1_s_016um_00287_00091-1"
> head(colnames(x1[["Spatial.008um"]]))
[1] "s_008um_00301_00321-1" "s_008um_00602_00290-1" "s_008um_00515_00112-1"
[4] "s_008um_00383_00696-1" "s_008um_00526_00291-1" "s_008um_00681_00396-1"

[ddiez]

This does not happen if we read one of the bin sizes only:

> x1 <- Load10X_Spatial("Mouse_Kidney", bin.size=8)
> x2 <- Load10X_Spatial("Visium_HD_Mouse_Brain", bin.size=8)
> x1 <- RenameCells(x1, add.cell.id="B1")
> x2 <- RenameCells(x2, add.cell.id="B2")
> x <- merge(x1, x2)
Warning message:
Key ‘slice1008um_’ taken, using ‘slice1008um2_’ instead

Session information:

> sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS

Matrix products: default
BLAS:   /media/diez/Backup/local/R-4.4.2/build/lib/libRblas.so 
LAPACK: /media/diez/Backup/local/R-4.4.2/build/lib/libRlapack.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=ja_JP.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=ja_JP.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=ja_JP.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=ja_JP.UTF-8 LC_IDENTIFICATION=C       

time zone: Asia/Tokyo
tzcode source: system (glibc)

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

other attached packages:
[1] Seurat_5.1.0       SeuratObject_5.0.2 sp_2.1-4

[... truncated ...]

[dcollins15]

@ddiez thanks for bringing this to our attention 🙂

The issue doesn't seem to be limited to VisiumHD datasets, I'm able to reproduce the error by merging any two datasets where:

1. At least one of the objects contains multiple assays
2. The two objects have overlapping cell names

In this case, CheckDuplicateCellNames will try to loop over each object.list and add a unique suffix onto the object's cell names, here. CheckDuplicateCellNames passed in a character vector of length ncol(object[[i]]) but this check inside RenameCells.Seurat seems to expect a vector of length ncol(object[[DefaultAssay(object)]]), hence the error.

I think this change may have been introduced to make the behavior of RenameCells.Seurat consistent with the new Cells.Seurat generic but it also seems to have broken CheckDuplicateNames 🤷 At any rate, we've added this bug to our backlog and we should have some bandwidth to resolve it in the next month or so. I'll let you know if/when there are any updates.

Thanks again

[ddiez]

@dcollins15 Excellent. Thanks for the additional information. I noticed while digging into the problem about the cell length mismatch but couldn't get enough knowledge at the time to figure out where it was coming from.