Issue reading in 10x Spatial Data

[wagnewsv]

Hello, I am having issues with the Load10x_Spatial() function. The error I am receiving is:
Image must be an object of class 'VisiumV1'.

The issue seems to partially stem from a separate package that defines the variable image, so that the statement if (is.null(x = image)) evaluates as false.
If I preset image=NULL, I can create a copy of the function that successfully loads in the data however the Load10x_Spatial function still produces the same error.

data_dir<-"/Users/willagnew-svoboda/Documents/Seurat_Visium_Tutorial"
list.files(data_dir)
Load10X_Spatial(data.dir = data_dir)

Output :

[1] "filtered_feature_bc_matrix.h5"
[2] "spatial"
Error in Load10X_Spatial(data.dir = data_dir) :
Image must be an object of class 'VisiumV1'.

sessionInfo:

sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

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

other attached packages:
[1] dplyr_1.1.3 patchwork_1.1.3
[3] ggplot2_3.4.3 stxBrain.SeuratData_0.1.1
[5] SeuratData_0.2.2.9001 Seurat_4.9.9.9060
[7] SeuratObject_4.9.9.9091 sp_2.0-0

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.15.0
[3] jsonlite_1.8.7 magrittr_2.0.3
[5] spatstat.utils_3.0-3 farver_2.1.1
[7] rmarkdown_2.24 vctrs_0.6.3
[9] ROCR_1.0-11 spatstat.explore_3.2-3
[11] htmltools_0.5.6 sctransform_0.3.5
[13] parallelly_1.36.0 KernSmooth_2.23-21
[15] htmlwidgets_1.6.2 ica_1.0-3
[17] plyr_1.8.8 plotly_4.10.2
[19] zoo_1.8-12 igraph_1.5.1
[21] mime_0.12 lifecycle_1.0.3
[23] pkgconfig_2.0.3 Matrix_1.5-4.1
[25] R6_2.5.1 fastmap_1.1.1
[27] fitdistrplus_1.1-11 future_1.33.0
[29] shiny_1.7.5 digest_0.6.33
[31] colorspace_2.1-0 tensor_1.5
[33] RSpectra_0.16-1 irlba_2.3.5.1
[35] labeling_0.4.3 progressr_0.14.0
[37] fansi_1.0.4 spatstat.sparse_3.0-2
[39] httr_1.4.7 polyclip_1.10-4
[41] abind_1.4-5 compiler_4.3.1
[43] remotes_2.4.2.1 bit64_4.0.5
[45] withr_2.5.0 fastDummies_1.7.3
[47] MASS_7.3-60 rappdirs_0.3.3
[49] tools_4.3.1 lmtest_0.9-40
[51] httpuv_1.6.11 future.apply_1.11.0
[53] goftest_1.2-3 glue_1.6.2
[55] nlme_3.1-162 promises_1.2.1
[57] grid_4.3.1 Rtsne_0.16
[59] cluster_2.1.4 reshape2_1.4.4
[61] generics_0.1.3 hdf5r_1.3.8
[63] gtable_0.3.4 spatstat.data_3.0-1
[65] tidyr_1.3.0 data.table_1.14.8
[67] utf8_1.2.3 spatstat.geom_3.2-5
[69] RcppAnnoy_0.0.21 ggrepel_0.9.3
[71] RANN_2.6.1 pillar_1.9.0
[73] stringr_1.5.0 spam_2.9-1
[75] RcppHNSW_0.4.1 later_1.3.1
[77] splines_4.3.1 lattice_0.21-8
[79] survival_3.5-5 bit_4.0.5
[81] deldir_1.0-9 tidyselect_1.2.0
[83] miniUI_0.1.1.1 pbapply_1.7-2
[85] knitr_1.43 gridExtra_2.3
[87] scattermore_1.2 xfun_0.40
[89] matrixStats_1.0.0 stringi_1.7.12
[91] lazyeval_0.2.2 yaml_2.3.7
[93] evaluate_0.21 codetools_0.2-19
[95] tibble_3.2.1 cli_3.6.1
[97] uwot_0.1.16 xtable_1.8-4
[99] reticulate_1.31 munsell_0.5.0
[101] Rcpp_1.0.11 globals_0.16.2
[103] spatstat.random_3.1-6 png_0.1-8
[105] parallel_4.3.1 ellipsis_0.3.2
[107] dotCall64_1.0-2 listenv_0.9.0
[109] viridisLite_0.4.2 scales_1.2.1
[111] ggridges_0.5.4 leiden_0.4.3
[113] purrr_1.0.2 crayon_1.5.2
[115] rlang_1.1.1 cowplot_1.1.1

[alikhuseynov]

this PR should solve it:

• Restore image argument to Load10X_Spatial() for seurat5 #7837