AttributeError occuring when reading in
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yanningzuo commented
Hi,
Thank you for putting together the HNOCA and I'm interested in comparing my brain organoid data to it. However, I encountered AttributeError: 'dict' object has no attribute 'dtype' when reading in and converting hnoca_pre-release_public_subset.h5ad to .rds. Below are my script, error messages and the session info. Thank you in advance for your help and please let me if there's any info needed.
ad <- import("anndata", convert = FALSE)
data_ad <- ad$read_h5ad("hnoca_pre-release_public_subset.h5ad")
# Error in py_call_impl(callable, call_args$unnamed, call_args$named) :
AttributeError: 'dict' object has no attribute 'dtype'
Run `reticulate::py_last_error()` for details.
── Python Exception Message ────────────────────────────────────────────────────
Traceback (most recent call last):
File "~/miniconda3/envs/r-reticulate/lib/python3.9/site-packages/anndata/readwrite/read.py", line 447, in read_h5ad
constructor_args = _read_args_from_h5ad(filename=filename, chunk_size=chunk_size)
File "~/miniconda3/envs/r-reticulate/lib/python3.9/site-packages/anndata/readwrite/read.py", line 502, in _read_args_from_h5ad
return AnnData._args_from_dict(d)
File "~/miniconda3/envs/r-reticulate/lib/python3.9/site-packages/anndata/core/anndata.py", line 2157, in _args_from_dict
if key in d_true_keys[true_key].dtype.names:
AttributeError: 'dict' object has no attribute 'dtype'
── R Traceback ─────────────────────────────────────────────────────────────────
▆
1. └─ad$read_h5ad("hnoca_pre-release_public_subset.h5ad")
2. └─reticulate:::py_call_impl(callable, call_args$unnamed, call_args$named)
sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
Matrix products: default
BLAS/LAPACK:~/miniconda3/lib/libopenblasp-r0.3.25.so; LAPACK version 3.11.0
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: America/Los_Angeles
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] unix_1.5.6 future_1.33.1 sceasy_0.0.7 reticulate_1.34.0
loaded via a namespace (and not attached):
[1] deldir_2.0-2 pbapply_1.7-2 gridExtra_2.3
[4] rlang_1.1.3 magrittr_2.0.3 RcppAnnoy_0.0.21
[7] matrixStats_1.2.0 ggridges_0.5.5 compiler_4.3.2
[10] spatstat.geom_3.2-7 png_0.1-8 vctrs_0.6.5
[13] reshape2_1.4.4 stringr_1.5.1 pkgconfig_2.0.3
[16] fastmap_1.1.1 ellipsis_0.3.2 utf8_1.2.4
[19] promises_1.2.1 purrr_1.0.2 jsonlite_1.8.8
[22] goftest_1.2-3 later_1.3.2 spatstat.utils_3.0-4
[25] irlba_2.3.5.1 parallel_4.3.2 cluster_2.1.6
[28] R6_2.5.1 ica_1.0-3 stringi_1.8.3
[31] RColorBrewer_1.1-3 spatstat.data_3.0-4 parallelly_1.36.0
[34] lmtest_0.9-40 scattermore_1.2 Rcpp_1.0.12
[37] tensor_1.5 future.apply_1.11.1 zoo_1.8-12
[40] sctransform_0.4.1 httpuv_1.6.13 Matrix_1.6-5
[43] splines_4.3.2 igraph_1.6.0 tidyselect_1.2.0
[46] abind_1.4-5 spatstat.random_3.2-2 codetools_0.2-19
[49] miniUI_0.1.1.1 spatstat.explore_3.2-5 listenv_0.9.0
[52] lattice_0.22-5 tibble_3.2.1 plyr_1.8.9
[55] shiny_1.8.0 withr_3.0.0 ROCR_1.0-11
[58] Rtsne_0.17 fastDummies_1.7.3 survival_3.5-7
[61] polyclip_1.10-6 fitdistrplus_1.1-11 pillar_1.9.0
[64] Seurat_5.0.1 KernSmooth_2.23-22 plotly_4.10.4
[67] generics_0.1.3 RcppHNSW_0.5.0 sp_2.1-2
[70] ggplot2_3.4.4 munsell_0.5.0 scales_1.3.0
[73] globals_0.16.2 xtable_1.8-4 glue_1.7.0
[76] lazyeval_0.2.2 tools_4.3.2 data.table_1.14.10
[79] RSpectra_0.16-1 RANN_2.6.1 leiden_0.4.3.1
[82] dotCall64_1.1-1 cowplot_1.1.2 grid_4.3.2
[85] tidyr_1.3.0 colorspace_2.1-0 nlme_3.1-164
[88] patchwork_1.2.0 cli_3.6.2 spatstat.sparse_3.0-3
[91] rappdirs_0.3.3 spam_2.10-0 fansi_1.0.6
[94] viridisLite_0.4.2 dplyr_1.1.4 uwot_0.1.16
[97] gtable_0.3.4 digest_0.6.34 progressr_0.14.0
[100] ggrepel_0.9.5 htmlwidgets_1.6.4 SeuratObject_5.0.1
[103] htmltools_0.5.7 lifecycle_1.0.4 httr_1.4.7
[106] mime_0.12 MASS_7.3-60