visium hd support

[raygozag]

Hi i'm trying to follow the visium hd tutorial but i keep trying to update my seurat installetion with

remotes::install_github("satijalab/seurat", "seurat5", quiet = TRUE) remotes::install_github("satijalab/seurat", "seurat5", quiet = TRUE, force=T) remotes::install_github("satijalab/seurat")

and reinstalled everything again too, but i still can't see the bin.size parameter. Even after restarting R or terminating the session.

object <- Load10X_Spatial(data.dir = localdir, bin.size =(8, 16))

Can anybody help me install the eversion for visium hd?

Thanks

`R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS

Matrix products: default BLAS/LAPACK: /opt/OpenBLAS/lib/libopenblas-r0.3.3.so; LAPACK version 3.8.0

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

time zone: America/Chicago tzcode source: system (glibc)

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

other attached packages: [1] dplyr_1.1.4 patchwork_1.2.0 ggplot2_3.5.1 Seurat_5.1.0 SeuratObject_5.0.2 sp_2.1-4

loaded via a namespace (and not attached): [1] deldir_2.0-4 pbapply_1.7-2 gridExtra_2.3 remotes_2.5.0 rlang_1.1.3 magrittr_2.0.3 RcppAnnoy_0.0.22 spatstat.geom_3.2-9
[9] matrixStats_1.3.0 ggridges_0.5.6 compiler_4.3.1 callr_3.7.6 png_0.1-8 vctrs_0.6.5 reshape2_1.4.4 hdf5r_1.3.10
[17] stringr_1.5.1 pkgconfig_2.0.3 fastmap_1.2.0 utf8_1.2.4 promises_1.3.0 rmarkdown_2.27 ps_1.7.6 bit_4.0.5
[25] purrr_1.0.2 xfun_0.44 jsonlite_1.8.8 goftest_1.2-3 later_1.3.2 spatstat.utils_3.0-4 irlba_2.3.5.1 parallel_4.3.1
[33] cluster_2.1.4 R6_2.5.1 ica_1.0-3 stringi_1.8.4 RColorBrewer_1.1-3 spatstat.data_3.0-4 reticulate_1.37.0 parallelly_1.37.1
[41] lmtest_0.9-40 scattermore_1.2 Rcpp_1.0.12 knitr_1.46 tensor_1.5 future.apply_1.11.2 zoo_1.8-12 sctransform_0.4.1
[49] httpuv_1.6.15 Matrix_1.6-4 splines_4.3.1 igraph_2.0.3 tidyselect_1.2.1 abind_1.4-5 rstudioapi_0.16.0 yaml_2.3.8
[57] spatstat.random_3.2-3 codetools_0.2-19 miniUI_0.1.1.1 spatstat.explore_3.2-7 processx_3.8.4 curl_5.2.1 pkgbuild_1.4.4 listenv_0.9.1
[65] lattice_0.21-8 tibble_3.2.1 plyr_1.8.9 withr_3.0.0 shiny_1.8.1.1 ROCR_1.0-11 evaluate_0.23 Rtsne_0.17
[73] desc_1.4.3 future_1.33.2 fastDummies_1.7.3 survival_3.5-5 polyclip_1.10-6 xml2_1.3.6 fitdistrplus_1.1-11 pillar_1.9.0
[81] KernSmooth_2.23-21 plotly_4.10.4 generics_0.1.3 RcppHNSW_0.6.0 munsell_0.5.1 scales_1.3.0 globals_0.16.3 xtable_1.8-4
[89] glue_1.7.0 lazyeval_0.2.2 tools_4.3.1 data.table_1.15.4 RSpectra_0.16-1 RANN_2.6.1 leiden_0.4.3.1 dotCall64_1.1-1
[97] cowplot_1.1.3 grid_4.3.1 tidyr_1.3.1 colorspace_2.1-0 nlme_3.1-162 cli_3.6.2 spatstat.sparse_3.0-3 spam_2.10-0
[105] fansi_1.0.6 viridisLite_0.4.2 gt_0.10.1 uwot_0.2.2 gtable_0.3.5 digest_0.6.35 progressr_0.14.0 ggrepel_0.9.5
[113] htmlwidgets_1.6.4 htmltools_0.5.8.1 lifecycle_1.0.4 httr_1.4.7 mime_0.12 bit64_4.0.5 MASS_7.3-60 `

[asmlgkj]

has you installed sucessfully? I did not

[zskylarli]

Hi - can you try to set thebin.sizeto a vector, like so?

object <- Load10X_Spatial(data.dir = localdir, bin.size = c(8, 16))

[raygozag]

that's not the issue. the problem is that the updated installation has no such parameter in the function. something is not updating even after forcing the update.

[dcollins15]

Have you tried installing via install.packages? (this is generally the preferred method)

remotes::install_github("satijalab/seurat", "seurat5", quiet = TRUE)
remotes::install_github("satijalab/seurat", "seurat5", quiet = TRUE, force=T)

Are both pointing to the pre-release seurat5 branch - it will not resolve to the correct version

remotes::install_github("satijalab/seurat")

Probably would've worked had you included force = TRUE

[zskylarli]

Closing this issue as there has been no activity, but feel free to reopen if further issues arise. Thanks!