test<-ReadH5MU("data_test.dir/pbmc_w3_teaseq.h5mu")
Error in dataset[[name]]$read() : attempt to apply non-function
import muon as mu
mu.read_h5mu("data_test.dir/pbmc_w3_teaseq.h5mu")
MuData object with n_obs × n_vars = 5805 × 113187
obs: 'sample', 'well', 'leiden_multiplex', 'leiden_mofa', 'leiden_wnn'
var: 'highly_variable', 'gene_ids', 'feature_types', 'genome', 'interval'
obsm: 'X_mofa', 'X_umap', 'X_wnn_umap'
varm: 'LFs'
obsp: 'mofa_connectivities', 'mofa_distances', 'wnn_connectivities', 'wnn_distances'
3 modalities
rna: 5805 x 16381
obs: 'n_genes_by_counts', 'total_counts', 'total_counts_mt', 'pct_counts_mt', 'leiden'
var: 'gene_ids', 'feature_types', 'genome', 'interval', 'mt', 'n_cells_by_counts', 'mean_counts', 'pct_dropout_by_counts', 'total_counts', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'hvg', 'leiden', 'leiden_colors', 'log1p', 'neighbors', 'pca', 'umap'
obsm: 'X_pca', 'X_umap'
varm: 'PCs'
layers: 'lognorm'
obsp: 'connectivities', 'distances'
atac: 5805 x 96760
obs: 'n_fragments', 'n_duplicate', 'n_mito', 'n_unique', 'altius_count', 'altius_frac', 'gene_bodies_count', 'gene_bodies_frac', 'peaks_count', 'peaks_frac', 'tss_count', 'tss_frac', 'barcodes', 'cell_name', 'well_id', 'chip_id', 'batch_id', 'pbmc_sample_id', 'DoubletScore', 'DoubletEnrichment', 'TSSEnrichment', 'n_genes_by_counts', 'total_counts', 'n_counts', 'leiden'
var: 'gene_ids', 'feature_types', 'genome', 'interval', 'n_cells_by_counts', 'mean_counts', 'pct_dropout_by_counts', 'total_counts', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
uns: 'hvg', 'leiden', 'leiden_colors', 'log1p', 'neighbors', 'pca', 'umap'
obsm: 'X_pca', 'X_umap'
varm: 'PCs'
layers: 'counts', 'lognorm'
obsp: 'connectivities', 'distances'
prot: 5805 x 46
obs: 'total_counts'
var: 'highly_variable'
uns: 'neighbors', 'pca', 'umap'
obsm: 'X_pca', 'X_umap'
varm: 'PCs'
layers: 'counts'
obsp: 'connectivities', 'distances'
I can explore the h5 but it breaks where the error says. it also seems to expect some attributes that I don't have in the mudata
h5 <- open_and_check_mudata("~/Documents/devel/data_test.dir/pbmc_w3_teaseq.h5mu")
metadata <- read_with_index(h5[["obs"]])
dataset = h5[['obs']]
dataset_attr <- tryCatch({
h5attributes(dataset)
}, error = function(e) {
list("_index" = "_index")
})
indexcol <- "_index"
if ("_index" %in% names(dataset_attr)) {
indexcol <- dataset_attr$`_index`
}
dataset_attr
columns <- names(dataset)
columns <- columns[columns != "__categories"]
columns
dataset[["sample"]]$read()
Error in dataset[[name]]$read() : attempt to apply non-function
values_attr <-h5attributes(dataset)
values_attr
$`column-order`
[1] "sample" "well"
$`_index`
[1] "_index"
$`encoding-type`
[1] "dataframe"
$`encoding-version`
[1] "0.2.0"
# so the following line will be NULL
# values_attr$categories
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur 11.3.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] bmcite.SeuratData_0.3.0 pbmc3k.SeuratData_3.1.4 SeuratData_0.2.2 hdf5r_1.3.5 MuDataSeurat_0.0.0.9000 magrittr_2.0.3 datapasta_3.1.0
[8] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.8 purrr_0.3.4 readr_2.1.2 tidyr_1.2.0 tibble_3.1.6
[15] ggplot2_3.3.5 tidyverse_1.3.1
loaded via a namespace (and not attached):
[1] readxl_1.4.0 backports_1.4.1 plyr_1.8.7 igraph_1.3.0 lazyeval_0.2.2 splines_4.1.2 listenv_0.8.0 scattermore_0.8
[9] digest_0.6.29 htmltools_0.5.2 fansi_1.0.3 tensor_1.5 cluster_2.1.3 ROCR_1.0-11 tzdb_0.3.0 remotes_2.4.2
[17] globals_0.14.0 modelr_0.1.8 matrixStats_0.62.0 spatstat.sparse_2.1-0 prettyunits_1.1.1 colorspace_2.0-3 rappdirs_0.3.3 rvest_1.0.2
[25] ggrepel_0.9.1 haven_2.4.3 callr_3.7.0 crayon_1.5.1 jsonlite_1.8.0 spatstat.data_2.1-4 survival_3.3-1 zoo_1.8-9
[33] glue_1.6.2 polyclip_1.10-0 gtable_0.3.0 leiden_0.3.9 clipr_0.8.0 pkgbuild_1.3.1 future.apply_1.8.1 abind_1.4-5
[41] scales_1.1.1 DBI_1.1.2 spatstat.random_2.2-0 miniUI_0.1.1.1 Rcpp_1.0.8.3 viridisLite_0.4.0 xtable_1.8-4 reticulate_1.24
[49] spatstat.core_2.4-2 bit_4.0.4 htmlwidgets_1.5.4 httr_1.4.2 anndata_0.7.5.3 RColorBrewer_1.1-3 ellipsis_0.3.2 Seurat_4.1.0
[57] ica_1.0-2 pkgconfig_2.0.3 uwot_0.1.11 dbplyr_2.1.1 deldir_1.0-6 utf8_1.2.2 tidyselect_1.1.2 rlang_1.0.2
[65] reshape2_1.4.4 later_1.3.0 munsell_0.5.0 cellranger_1.1.0 tools_4.1.2 cli_3.3.0 generics_0.1.2 broom_0.7.12
[73] ggridges_0.5.3 fastmap_1.1.0 goftest_1.2-3 processx_3.5.3 bit64_4.0.5 fs_1.5.2 fitdistrplus_1.1-8 RANN_2.6.1
[81] pbapply_1.5-0 future_1.24.0 nlme_3.1-157 mime_0.12 formatR_1.12 xml2_1.3.3 compiler_4.1.2 rstudioapi_0.13
[89] plotly_4.10.0 curl_4.3.2 png_0.1-7 spatstat.utils_2.3-0 reprex_2.0.1 stringi_1.7.6 ps_1.6.0 lattice_0.20-45
[97] Matrix_1.4-1 SeuratDisk_0.0.0.9019 vctrs_0.3.8 pillar_1.7.0 lifecycle_1.0.1 spatstat.geom_2.4-0 lmtest_0.9-40 RcppAnnoy_0.0.19
[105] addinexamples_0.1.0 data.table_1.14.2 cowplot_1.1.1 irlba_2.3.5 httpuv_1.6.5 patchwork_1.1.1 R6_2.5.1 promises_1.2.0.1
[113] KernSmooth_2.23-20 gridExtra_2.3 parallelly_1.31.0 codetools_0.2-18 MASS_7.3-56 assertthat_0.2.1 rprojroot_2.0.3 withr_2.5.0
[121] SeuratObject_4.0.4 sctransform_0.3.3 mgcv_1.8-40 parallel_4.1.2 hms_1.1.1 grid_4.1.2 rpart_4.1.16 Rtsne_0.15
[129] shiny_1.7.1 lubridate_1.8.0
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