pacman::p_load(Seurat, tidyverse, qs2, SingleCellExperiment, zellkonverter)
knitr::opts_knit$set(root.dir = "/home/han/Desktop/guoqiang/stroke_bm/stroke_bm_Rproj")
setwd("/home/han/Desktop/guoqiang/stroke_bm/stroke_bm_Rproj")
source("codes/functions.R")Cell Type Prediction
导出 h5ad，供下一篇 CellTypist 使用。
file_path <- "celltypist"
if (!dir.exists(file_path)) {
dir.create(file_path, recursive = TRUE)
}seurat_object <-
qs_read(
"data/rdata/dim_reduction/seurat_object_clustered.qs2",
nthreads = 10
)
DefaultAssay(seurat_object)[1] "RNA"Layers(seurat_object)[1] "counts" "data" "scale.data"# seurat_object <-
# seurat_object |>
# JoinLayers()seurat_object[["RNA"]]$counts <-
as(seurat_object[["RNA"]]$counts, Class = "dgCMatrix")
seurat_object[["RNA"]]$data <- NULL
seurat_object[["RNA"]]$scale.data <- NULLseurat_object <- as.SingleCellExperiment(seurat_object, assay = c("RNA"))writeH5AD(
seurat_object,
"celltypist/seurat_object.h5ad",
X_name = "counts"
)sessionInfo()R version 4.4.3 (2025-02-28)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.3 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.12.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Asia/Shanghai
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] zellkonverter_1.16.0 SingleCellExperiment_1.28.1
[3] SummarizedExperiment_1.36.0 Biobase_2.66.0
[5] GenomicRanges_1.58.0 GenomeInfoDb_1.42.0
[7] IRanges_2.40.0 S4Vectors_0.44.0
[9] BiocGenerics_0.52.0 MatrixGenerics_1.18.0
[11] matrixStats_1.4.1 qs2_0.1.7
[13] lubridate_1.9.3 forcats_1.0.0
[15] stringr_1.5.1 dplyr_1.1.4
[17] purrr_1.0.2 readr_2.1.5
[19] tidyr_1.3.1 tibble_3.2.1
[21] ggplot2_3.5.1 tidyverse_2.0.0
[23] Seurat_5.2.1 SeuratObject_5.0.2
[25] sp_2.1-4
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 jsonlite_1.8.9 magrittr_2.0.3
[4] spatstat.utils_3.1-1 farver_2.1.2 rmarkdown_2.29
[7] zlibbioc_1.52.0 vctrs_0.6.5 ROCR_1.0-11
[10] spatstat.explore_3.3-3 S4Arrays_1.6.0 htmltools_0.5.8.1
[13] SparseArray_1.6.0 sctransform_0.4.1 parallelly_1.39.0
[16] KernSmooth_2.23-26 basilisk_1.18.0 htmlwidgets_1.6.4
[19] ica_1.0-3 plyr_1.8.9 plotly_4.10.4
[22] zoo_1.8-12 igraph_2.1.2 mime_0.12
[25] lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.7-3
[28] R6_2.5.1 fastmap_1.2.0 GenomeInfoDbData_1.2.13
[31] fitdistrplus_1.2-1 future_1.34.0 shiny_1.9.1
[34] digest_0.6.37 colorspace_2.1-1 patchwork_1.3.0
[37] tensor_1.5 RSpectra_0.16-2 irlba_2.3.5.1
[40] filelock_1.0.3 progressr_0.15.1 fansi_1.0.6
[43] spatstat.sparse_3.1-0 timechange_0.3.0 httr_1.4.7
[46] polyclip_1.10-7 abind_1.4-8 compiler_4.4.3
[49] withr_3.0.2 fastDummies_1.7.4 MASS_7.3-65
[52] DelayedArray_0.32.0 tools_4.4.3 lmtest_0.9-40
[55] httpuv_1.6.15 future.apply_1.11.3 goftest_1.2-3
[58] glue_1.8.0 nlme_3.1-166 promises_1.3.2
[61] grid_4.4.3 Rtsne_0.17 cluster_2.1.8.1
[64] reshape2_1.4.4 generics_0.1.3 gtable_0.3.6
[67] spatstat.data_3.1-4 tzdb_0.4.0 data.table_1.16.2
[70] hms_1.1.3 XVector_0.46.0 stringfish_0.18.0
[73] utf8_1.2.4 spatstat.geom_3.3-4 RcppAnnoy_0.0.22
[76] ggrepel_0.9.6 RANN_2.6.2 pillar_1.9.0
[79] spam_2.11-0 RcppHNSW_0.6.0 later_1.4.1
[82] splines_4.4.3 lattice_0.22-6 survival_3.8-3
[85] deldir_2.0-4 tidyselect_1.2.1 miniUI_0.1.1.1
[88] pbapply_1.7-2 knitr_1.49 gridExtra_2.3
[91] scattermore_1.2 xfun_0.49 UCSC.utils_1.2.0
[94] stringi_1.8.4 lazyeval_0.2.2 yaml_2.3.10
[97] pacman_0.5.1 evaluate_1.0.1 codetools_0.2-20
[100] cli_3.6.3 uwot_0.2.2 RcppParallel_5.1.9
[103] xtable_1.8-4 reticulate_1.42.0 munsell_0.5.1
[106] Rcpp_1.0.13-1 dir.expiry_1.14.0 globals_0.16.3
[109] spatstat.random_3.3-2 png_0.1-8 spatstat.univar_3.1-1
[112] parallel_4.4.3 basilisk.utils_1.18.0 dotCall64_1.2
[115] listenv_0.9.1 viridisLite_0.4.2 scales_1.3.0
[118] ggridges_0.5.6 crayon_1.5.3 rlang_1.1.4
[121] cowplot_1.1.3