get_seurat() gets scvi embedding in 2023-12-15 Census, but not in 2024-07-01 or 2025-01-30 versions #1393
Description
This code works for old 2023-12-15 version of Census
require(Seurat)
require(cellxgene.census)
census_version <- "2023-12-15" # 2023-12-15 embeddings work in get_seurat(); 2024-07-01 & 2025-01-30 embeddings do NOT work
organism <- "homo_sapiens"
my_obs <- "sex == 'male' & is_primary_data == TRUE & disease == 'COVID-19' & tissue_general == 'blood' & cell_type == 'CD14-positive, CD16-positive monocyte'"
census <- open_soma(census_version = census_version)
s <- get_seurat(
census = census,
organism = organism,
obs_value_filter = my_obs,
obsm_layers = c("scvi")
)
... but does NOT work in any recent Census version, like 2024-07-01 or 2025-01-30
get_seurat() produces warning
Warning: No reductions found
Expected behavior
Embeddings (scvi, geneformer, scgpt, etc..) will be accessible in the most recent Census
Environment
sessionInfo()
R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
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
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] cellxgene.census_1.16.1 Seurat_5.3.0 SeuratObject_5.1.0 sp_2.2-0
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.17.1 jsonlite_2.0.0 magrittr_2.0.3 spatstat.utils_3.1-3 farver_2.1.2 rmarkdown_2.29
[8] fs_1.6.6 vctrs_0.6.5 ROCR_1.0-11 spatstat.explore_3.4-2 base64enc_0.1-3 htmltools_0.5.8.1 curl_6.2.2
[15] sctransform_0.4.2 parallelly_1.43.0 KernSmooth_2.23-26 htmlwidgets_1.6.4 ica_1.0-3 plyr_1.8.9 plotly_4.10.4
[22] zoo_1.8-14 igraph_2.1.4 mime_0.13 lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.7-3 R6_2.6.1
[29] fastmap_1.2.0 fitdistrplus_1.2-2 future_1.40.0 shiny_1.10.0 digest_0.6.37 colorspace_2.1-1 tiledb_0.31.1
[36] patchwork_1.3.0 tensor_1.5 RSpectra_0.16-2 irlba_2.3.5.1 aws.signature_0.6.0 progressr_0.15.1 urltools_1.7.3
[43] spatstat.sparse_3.1-0 httr_1.4.7 polyclip_1.10-7 abind_1.4-8 compiler_4.5.0 bit64_4.6.0-1 withr_3.0.2
[50] fastDummies_1.7.5 MASS_7.3-65 tiledbsoma_1.16.1 tools_4.5.0 lmtest_0.9-40 httpuv_1.6.16 future.apply_1.11.3
[57] goftest_1.2-3 glue_1.8.0 nlme_3.1-168 promises_1.3.2 grid_4.5.0 rsconnect_1.3.4 Rtsne_0.17
[64] cluster_2.1.8.1 reshape2_1.4.4 generics_0.1.3 gtable_0.3.6 spatstat.data_3.1-6 tidyr_1.3.1 data.table_1.17.0
[71] xml2_1.3.8 spatstat.geom_3.3-6 RcppAnnoy_0.0.22 ggrepel_0.9.6 RANN_2.6.2 pillar_1.10.2 stringr_1.5.1
[78] spam_2.11-1 nanoarrow_0.6.0-1 RcppHNSW_0.6.0 later_1.4.2 splines_4.5.0 dplyr_1.1.4 lattice_0.22-7
[85] survival_3.8-3 bit_4.6.0 deldir_2.0-4 tidyselect_1.2.1 miniUI_0.1.2 pbapply_1.7-2 knitr_1.50
[92] gridExtra_2.3 RcppCCTZ_0.2.13 scattermore_1.2 xfun_0.52 matrixStats_1.5.0 stringi_1.8.7 lazyeval_0.2.2
[99] yaml_2.3.10 evaluate_1.0.3 codetools_0.2-20 tibble_3.2.1 cli_3.6.5 uwot_0.2.3 arrow_19.0.1.1
[106] xtable_1.8-4 reticulate_1.42.0 dichromat_2.0-0.1 Rcpp_1.0.14 globals_0.17.0 spatstat.random_3.3-3 triebeard_0.4.1
[113] RcppSpdlog_0.0.21 png_0.1-8 spatstat.univar_3.1-2 parallel_4.5.0 ggplot2_3.5.2 assertthat_0.2.1 dotCall64_1.2
[120] aws.s3_0.3.21 spdl_0.0.5 listenv_0.9.1 viridisLite_0.4.2 scales_1.4.0 ggridges_0.5.6 purrr_1.0.4
[127] rlang_1.1.6 cowplot_1.1.3 nanotime_0.3.12