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20 hours ago •
mojaveazure
mojaveazure
Error when saving a Visium Seurat to H5Seurat
Hi I got this error running
SaveH5Seurat(Plasticity_spatial, overwrite = TRUE)
Creating h5Seurat file for version 3.1.5.9900
Adding counts for Spatial
Adding data for Spatial
No variable features found for Spatial
No feature-level metadata found for Spatial
Adding counts for SCT
Adding data for SCT
Adding scale.data for SCT
Adding variable features for SCT
No feature-level metadata found for SCT
Writing out SCTModel.list for SCT
Adding data for integrated
Adding scale.data for integrated
Adding variable features for integrated
No feature-level metadata found for integrated
Writing out SCTModel.list for integrated
Adding data for prediction.Cell_subtype
No variable features found for prediction.Cell_subtype
No feature-level metadata found for prediction.Cell_subtype
Adding data for prediction.Cell_type
No variable features found for prediction.Cell_type
No feature-level metadata found for prediction.Cell_type
Adding cell embeddings for pca
Adding loadings for pca
No projected loadings for pca
Adding standard deviations for pca
No JackStraw data for pca
Adding cell embeddings for umap
No loadings for umap
No projected loadings for umap
No standard deviations for umap
No JackStraw data for umap
Adding image P19
Adding image P27
Adding image P37
Adding image P58
Adding image P59
Adding image P69
Adding image P75
Error in guess_dtype(x = x, ...) : unknown type
My object is :
An object of class Seurat
39218 features across 34047 samples within 5 assays
Active assay: SCT (18070 features, 3000 variable features)
4 other assays present: Spatial, integrated, prediction.Cell_subtype, prediction.Cell_type
2 dimensional reductions calculated: pca, umap
7 images present: P19, P27, P37, P58, P59, P69, P75
How can I solve this ?
sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4
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: Europe/Paris
tzcode source: internal
attached base packages:
[1] parallel grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] SeuratDisk_0.0.0.9020 matrixStats_0.63.0 rlist_0.4.6.2 ReactomePA_1.44.0
[5] harmony_0.1.1 Rcpp_1.0.10 data.table_1.14.8 UCell_2.4.0
[9] BiocParallel_1.34.1 clusterProfiler_4.8.1 ComplexHeatmap_2.16.0 lubridate_1.9.2
[13] forcats_1.0.0 stringr_1.5.0 dplyr_1.1.2 purrr_1.0.1
[17] readr_2.1.4 tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.2
[21] tidyverse_2.0.0 SeuratObject_4.1.3 Seurat_4.3.0 qs_0.25.5
loaded via a namespace (and not attached):
[1] spatstat.sparse_3.0-1 bitops_1.0-7 enrichplot_1.20.0
[4] HDO.db_0.99.1 httr_1.4.6 RColorBrewer_1.1-3
[7] doParallel_1.0.17 tools_4.3.0 sctransform_0.3.5
[10] utf8_1.2.3 R6_2.5.1 lazyeval_0.2.2
[13] uwot_0.1.14 GetoptLong_1.0.5 withr_2.5.0
[16] sp_1.6-0 graphite_1.46.0 gridExtra_2.3
[19] progressr_0.13.0 cli_3.6.1 Biobase_2.60.0
[22] spatstat.explore_3.2-1 scatterpie_0.1.9 spatstat.data_3.0-1
[25] ggridges_0.5.4 pbapply_1.7-0 yulab.utils_0.0.6
[28] gson_0.1.0 DOSE_3.26.1 parallelly_1.35.0
[31] rstudioapi_0.14 RSQLite_2.3.1 generics_0.1.3
[34] gridGraphics_0.5-1 shape_1.4.6 RApiSerialize_0.1.2
[37] ica_1.0-3 spatstat.random_3.1-5 zip_2.3.0
[40] GO.db_3.17.0 Matrix_1.5-4 fansi_1.0.4
[43] S4Vectors_0.38.1 abind_1.4-5 lifecycle_1.0.3
[46] yaml_2.3.7 SummarizedExperiment_1.30.1 qvalue_2.32.0
[49] Rtsne_0.16 blob_1.2.4 promises_1.2.0.1
[52] crayon_1.5.2 miniUI_0.1.1.1 lattice_0.21-8
[55] cowplot_1.1.1 KEGGREST_1.40.0 pillar_1.9.0
[58] knitr_1.42 fgsea_1.26.0 GenomicRanges_1.52.0
[61] rjson_0.2.21 future.apply_1.10.0 codetools_0.2-19
[64] fastmatch_1.1-3 leiden_0.4.3 glue_1.6.2
[67] downloader_0.4 ggfun_0.0.9 remotes_2.4.2
[70] vctrs_0.6.2 png_0.1-8 treeio_1.24.0
[73] gtable_0.3.3 cachem_1.0.8 xfun_0.39
[76] openxlsx_4.2.5.2 S4Arrays_1.0.1 mime_0.12
[79] tidygraph_1.2.3 survival_3.5-5 SingleCellExperiment_1.22.0
[82] iterators_1.0.14 ellipsis_0.3.2 fitdistrplus_1.1-11
[85] ROCR_1.0-11 nlme_3.1-162 ggtree_3.8.0
[88] bit64_4.0.5 RcppAnnoy_0.0.20 GenomeInfoDb_1.36.0
[91] irlba_2.3.5.1 KernSmooth_2.23-21 colorspace_2.1-0
[94] BiocGenerics_0.46.0 DBI_1.1.3 tidyselect_1.2.0
[97] bit_4.0.5 compiler_4.3.0 graph_1.78.0
[100] BiocNeighbors_1.18.0 hdf5r_1.3.8 DelayedArray_0.26.2
[103] plotly_4.10.1 stringfish_0.15.7 shadowtext_0.1.2
[106] scales_1.2.1 lmtest_0.9-40 rappdirs_0.3.3
[109] digest_0.6.31 goftest_1.2-3 spatstat.utils_3.0-3
[112] rmarkdown_2.21 XVector_0.40.0 htmltools_0.5.5
[115] pkgconfig_2.0.3 MatrixGenerics_1.12.0 fastmap_1.1.1
[118] rlang_1.1.1 GlobalOptions_0.1.2 htmlwidgets_1.6.2
[121] shiny_1.7.4 farver_2.1.1 zoo_1.8-12
[124] jsonlite_1.8.4 GOSemSim_2.26.0 RCurl_1.98-1.12
[127] magrittr_2.0.3 GenomeInfoDbData_1.2.10 ggplotify_0.1.0
[130] patchwork_1.1.2 munsell_0.5.0 ape_5.7-1
[133] viridis_0.6.3 reticulate_1.28 stringi_1.7.12
[136] ggraph_2.1.0 zlibbioc_1.46.0 MASS_7.3-60
[139] plyr_1.8.8 listenv_0.9.0 ggrepel_0.9.3
[142] deldir_1.0-6 Biostrings_2.68.0 graphlayouts_1.0.0
[145] splines_4.3.0 tensor_1.5 hms_1.1.3
[148] circlize_0.4.15 igraph_1.4.2 spatstat.geom_3.2-1
[151] reshape2_1.4.4 stats4_4.3.0 evaluate_0.21
[154] RcppParallel_5.1.7 tzdb_0.4.0 foreach_1.5.2
[157] tweenr_2.0.2 httpuv_1.6.11 RANN_2.6.1
[160] polyclip_1.10-4 future_1.32.0 clue_0.3-64
[163] scattermore_1.0 ggforce_0.4.1 xtable_1.8-4
[166] reactome.db_1.84.0 tidytree_0.4.2 later_1.3.1
[169] viridisLite_0.4.2 aplot_0.1.10 memoise_2.0.1
[172] AnnotationDbi_1.62.1 IRanges_2.34.0 cluster_2.1.4
[175] timechange_0.2.0 globals_0.16.2
I found the problem. it's was the misc slot with a ggplot2 object inside
I found the problem. it's was the misc slot with a ggplot2 object inside hi how do you solved this?
