Problem in loading spaceranger output in seurat

[Enrico940]

Hi Seurat dev team and thank you for the great package you developed!
I am following your tutorial for spatial transcriptomic. I ran spaceranger pipeline as described in the main page of spaceranger (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/tutorials/count-ff-tutorial). I tried to upload the outs in R with Load10X_Saptial function and I found that one of the file is not correctly named to load in Seurat (tissue_positions.csv need to be changed in tissue_positions_list.csv)

Load10X_Spatial("./V1_Adult_Mouse_Brain/outs")
Error in file(file, "rt") : cannot open the connection
In addition: Warning messages:
1: In sparseMatrix(i = indices[] + 1, p = indptr[], x = as.numeric(x = counts[]), :
'giveCsparse' has been deprecated; setting 'repr = "T"' for you
2: In file(file, "rt") :
cannot open file './V1_Adult_Mouse_Brain/outs/spatial/tissue_positions_list.csv': No such file or directory

I changed the name in tissue_positions_list.csv and it seems solved since I am now able to create the seurat object. However, when I try to run SpatialFeaturePlot it returns me an error. Can you help me to solve it ? The same error is also reproducible with the latest version of Seurat 4.0.6

se = Load10X_Spatial("./V1_Adult_Mouse_Brain/outs")
Warning message:
In sparseMatrix(i = indices[] + 1, p = indptr[], x = as.numeric(x = counts[]), :
'giveCsparse' has been deprecated; setting 'repr = "T"' for you

SpatialFeaturePlot(se, features = "nCount_Spatial")
Error in FUN(left, right) : non-numeric argument to binary operator

sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

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

other attached packages:
[1] STutility_0.1.0 ggplot2_3.3.3 SeuratObject_4.0.2 Seurat_4.0.4

loaded via a namespace (and not attached):
[1] nlme_3.1-152 matrixStats_0.61.0 spatstat.sparse_2.0-0
[4] bit64_4.0.5 RcppAnnoy_0.0.19 RColorBrewer_1.1-2
[7] httr_1.4.2 sctransform_0.3.3 tools_4.0.3
[10] utf8_1.2.1 R6_2.5.1 irlba_2.3.3
[13] rpart_4.1-15 KernSmooth_2.23-20 uwot_0.1.10
[16] mgcv_1.8-34 DBI_1.1.1 lazyeval_0.2.2
[19] colorspace_2.0-2 raster_3.4-13 sp_1.4-5
[22] readbitmap_0.1.5 withr_2.4.1 tidyselect_1.1.0
[25] gridExtra_2.3 bit_4.0.4 compiler_4.0.3
[28] hdf5r_1.3.3 shinyjs_2.1.0 plotly_4.9.3
[31] scales_1.1.1 lmtest_0.9-38 spatstat.data_2.1-0
[34] ggridges_0.5.3 pbapply_1.5-0 tiff_0.1-11
[37] goftest_1.2-2 stringr_1.4.0 digest_0.6.28
[40] spatstat.utils_2.3-0 jpeg_0.1-9 pkgconfig_2.0.3
[43] htmltools_0.5.1.1 parallelly_1.28.1 fastmap_1.1.0
[46] htmlwidgets_1.5.3 rlang_0.4.10 shiny_1.6.0
[49] generics_0.1.0 zoo_1.8-9 jsonlite_1.7.2
[52] ica_1.0-2 dplyr_1.0.5 magrittr_2.0.1
[55] patchwork_1.1.1 Matrix_1.3-4 Rcpp_1.0.7
[58] munsell_0.5.0 fansi_0.5.0 abind_1.4-5
[61] reticulate_1.20 lifecycle_1.0.0 stringi_1.5.3
[64] MASS_7.3-54 Rtsne_0.15 plyr_1.8.6
[67] grid_4.0.3 parallel_4.0.3 listenv_0.8.0
[70] promises_1.2.0.1 ggrepel_0.9.1 crayon_1.4.1
[73] miniUI_0.1.1.1 deldir_1.0-6 lattice_0.20-45
[76] cowplot_1.1.1 splines_4.0.3 tensor_1.5
[79] magick_2.7.2 zeallot_0.1.0 pillar_1.6.0
[82] igraph_1.2.6 spatstat.geom_2.3-2 imager_0.42.13
[85] future.apply_1.7.0 reshape2_1.4.4 codetools_0.2-18
[88] leiden_0.3.7 glue_1.4.2 bmp_0.3
[91] data.table_1.14.2 png_0.1-7 vctrs_0.3.7
[94] httpuv_1.5.5 gtable_0.3.0 RANN_2.6.1
[97] purrr_0.3.4 spatstat.core_2.0-0 polyclip_1.10-0
[100] tidyr_1.1.3 scattermore_0.7 future_1.21.0
[103] assertthat_0.2.1 mime_0.12 xtable_1.8-4
[106] later_1.1.0.1 survival_3.2-10 viridisLite_0.4.0
[109] tibble_3.1.0 cluster_2.1.2 globals_0.14.0
[112] fitdistrplus_1.1-3 ellipsis_0.3.1 ROCR_1.0-11

[samuel-marsh]

Hi,

Not member of dev team but hopefully can be helpful. There was recently update to dev branch to accommodate changes made in SpaceRanger 2.0 (#6208). Does updating to the dev branch and re-running your code (without renaming the file) solve the issues you are having?

Best,
Sam

[bsteglich]

I ran into the same problem, updating to dev branch did not solve it. When I compared my data set with the brain data set from the tutorial, I noticed that the image coordinates of my data set (Seuratobj@images$slice1@coordinates) were all stored as characters. Converting them into numeric solved the issue.

[Enrico940]

Thank you all for your reply! Yes now is working as suggested by bsteglich. However they need to update it !