why the SCopeLoomR showing not get_regulons function
honghh2018 opened this issue · 4 comments
honghh2018 commented
Hi @ALL,
The error occurred when runing below code,
library(SCENIC)
library(SCopeLoomR)
loom <- open_loom('pyscenic_process.loom')
regulons_incidMat <- get_regulons(loom)
Even though the get_regulons export from package SCopeLoomR, it still say no this function
how to fix this issue?
The SCopeLoomR detail:
Best,
hanhuihong
honghh2018 commented
Hi @ALL,
This question had solved with the ScopeLoomR package compiled with higher version h5cc.
Thanks
honghh2018 commented
There another issue about the loom file using below code to transform ex_matrix,auc_mtx and regulons into loom when loading the loom file into R encounter error.
export2loom(
ex_mtx = ex_matrix,
auc_mtx = auc_mtx,
regulons = [r.rename(r.name.replace('(+)',' ('+str(len(r))+'g)')) for r in regulons],
out_fname = "/share/nas1/Data/Users/honghh/Personality/2020-3-31/Re_Analysis2020-8-7/pySCENIC/analysis/latest_docker_for_transpose_matrix//pyscenic_process.loom"
)
Error in get_regulons(loom) :
The attribute 'MotifRegulons' is not available in this loom file. Possible values include: Regulons. Try setting the 'attrName' argument to one of these values (i.e., get_regulons(loom, attrName='Regulons'))
the sessioninfo showing below:
R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=zh_CN.UTF-8 LC_NUMERIC=C LC_TIME=zh_CN.UTF-8
[4] LC_COLLATE=zh_CN.UTF-8 LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=zh_CN.UTF-8
[7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] SCopeLoomR_0.9.3 SCENIC_1.1.2-01 RColorBrewer_1.1-2
[4] doParallel_1.0.15 iterators_1.0.12 foreach_1.4.7
[7] cowplot_1.0.0 NMF_0.23.0 bigmemory_4.5.36
[10] cluster_2.1.0 rngtools_1.5 pkgmaker_0.31.1
[13] registry_0.5-1 org.Hs.eg.db_3.10.0 AnnotationDbi_1.48.0
[16] clusterProfiler_3.14.3 circlize_0.4.10 plyr_1.8.5
[19] export_0.2.2 gdtools_0.2.1 shiny_1.4.0
[22] monocle3_0.2.0 SingleCellExperiment_1.8.0 SummarizedExperiment_1.16.1
[25] DelayedArray_0.12.1 BiocParallel_1.20.1 matrixStats_0.55.0
[28] GenomicRanges_1.38.0 GenomeInfoDb_1.22.0 IRanges_2.20.1
[31] S4Vectors_0.24.1 Biobase_2.46.0 ggplot2_3.3.2
[34] dplyr_1.0.2 stringr_1.4.0 BiocGenerics_0.32.0
[37] data.table_1.12.8 ComplexHeatmap_2.4.3 Signac_1.0.0
[40] infercnv_1.2.1 Seurat_3.2.0
loaded via a namespace (and not attached):
[1] rgl_0.100.30 rsvd_1.0.2 Hmisc_4.3-0 ica_1.0-2
[5] RcppRoll_0.3.0 Rsamtools_2.2.2 lmtest_0.9-37 crayon_1.3.4
[9] MASS_7.3-51.5 nlme_3.1-143 backports_1.1.5 GOSemSim_2.12.0
[13] rlang_0.4.7 argparse_2.0.1 XVector_0.26.0 ROCR_1.0-7
[17] irlba_2.3.3 limma_3.42.0 flextable_0.5.6 rjson_0.2.20
[21] manipulateWidget_0.10.0 bit64_0.9-7 glue_1.4.1 pheatmap_1.0.12
[25] sctransform_0.2.1 DOSE_3.12.0 tidyselect_1.1.0 fitdistrplus_1.0-14
[29] XML_3.98-1.20 tidyr_1.0.0 zoo_1.8-6 GenomicAlignments_1.22.1
[33] xtable_1.8-4 magrittr_1.5 evaluate_0.14 bibtex_0.4.2.1
[37] cli_2.0.0 zlibbioc_1.32.0 rstudioapi_0.10 miniUI_0.1.1.1
[41] rjags_4-10 rpart_4.1-15 fastmatch_1.1-0 ensembldb_2.10.2
[45] lambda.r_1.2.4 xfun_0.11 askpass_1.1 clue_0.3-57
[49] caTools_1.17.1.3 tidygraph_1.1.2 tibble_2.1.3 ggrepel_0.8.1
[53] biovizBase_1.34.1 ape_5.3 listenv_0.8.0 Biostrings_2.54.0
[57] png_0.1-7 reshape_0.8.8 future_1.15.1 withr_2.1.2
[61] lsa_0.73.2 bitops_1.0-6 ggforce_0.3.1 RBGL_1.62.1
[65] GSEABase_1.48.0 AnnotationFilter_1.10.0 coda_0.19-3 pillar_1.4.3
[69] RcppParallel_4.4.4 gplots_3.0.1.1 GlobalOptions_0.1.2 GenomicFeatures_1.38.1
[73] multcomp_1.4-11 hdf5r_1.3.2 GetoptLong_1.0.2 europepmc_0.3
[77] vctrs_0.3.2 generics_0.0.2 urltools_1.7.3 tools_3.6.0
[81] foreign_0.8-74 munsell_0.5.0 tweenr_1.0.1 fgsea_1.12.0
[85] fastmap_1.0.1 compiler_3.6.0 abind_1.4-5 httpuv_1.5.2
[89] rtracklayer_1.46.0 plotly_4.9.1 GenomeInfoDbData_1.2.2 gridExtra_2.3
[93] edgeR_3.28.0 lattice_0.20-38 deldir_0.1-23 later_1.0.0
[97] BiocFileCache_1.10.2 jsonlite_1.6 GGally_1.4.0 scales_1.1.0
[101] graph_1.64.0 pbapply_1.4-2 lazyeval_0.2.2 promises_1.1.0
[105] spatstat_1.63-3 R.utils_2.9.2 latticeExtra_0.6-29 goftest_1.2-2
[109] spatstat.utils_1.17-0 reticulate_1.14 checkmate_2.0.0 openxlsx_4.1.4
[113] rmarkdown_2.0 sandwich_2.5-1 webshot_0.5.2 stargazer_5.2.2
[117] Rtsne_0.15 dichromat_2.0-0 BSgenome_1.54.0 uwot_0.1.5
[121] igraph_1.2.4.2 yaml_2.2.0 survival_3.1-8 systemfonts_0.1.1
[125] htmltools_0.4.0 memoise_1.1.0 VariantAnnotation_1.32.0 modeltools_0.2-22
[129] locfit_1.5-9.1 graphlayouts_0.5.0 viridisLite_0.3.0 digest_0.6.23
[133] assertthat_0.2.1 mime_0.8 rappdirs_0.3.1 futile.options_1.0.1
[137] npsurv_0.4-0 bigmemory.sri_0.1.3 RSQLite_2.1.5 future.apply_1.3.0
[141] lsei_1.2-0 blob_1.2.0 R.oo_1.23.0 futile.logger_1.4.3
[145] splines_3.6.0 Formula_1.2-3 OrganismDbi_1.28.0 ProtGenerics_1.18.0
[149] RCurl_1.95-4.12 broom_0.5.3 hms_0.5.2 colorspace_1.4-1
[153] base64enc_0.1-3 BiocManager_1.30.10 shape_1.4.4 libcoin_1.0-5
[157] findpython_1.0.5 nnet_7.3-12 Rcpp_1.0.3 coin_1.3-1
[161] RANN_2.6.1 mvtnorm_1.0-11 enrichplot_1.6.1 ggseqlogo_0.1
[165] fansi_0.4.0 SnowballC_0.7.0 R6_2.4.1 ggridges_0.5.1
[169] lifecycle_0.2.0 acepack_1.4.1 formatR_1.7 zip_2.0.4
[173] curl_4.3 gdata_2.18.0 leiden_0.3.1 fastcluster_1.1.25
[177] DO.db_2.9 Matrix_1.2-18 qvalue_2.18.0 ggbio_1.34.0
[181] RcppAnnoy_0.0.14 TH.data_1.0-10 htmlwidgets_1.5.1 officer_0.3.6
[185] polyclip_1.10-0 triebeard_0.3.0 biomaRt_2.42.0 purrr_0.3.3
[189] crosstalk_1.0.0 gridGraphics_0.4-1 mgcv_1.8-31 globals_0.12.5
[193] openssl_1.4.1 htmlTable_1.13.3 patchwork_1.0.0 codetools_0.2-16
[197] GO.db_3.10.0 gtools_3.8.1 prettyunits_1.0.2 dbplyr_1.4.2
[201] R.methodsS3_1.7.1 gridBase_0.4-7 gtable_0.3.0 DBI_1.1.0
[205] tensor_1.5 httr_1.4.1 KernSmooth_2.23-16 stringi_1.4.3
[209] progress_1.2.2 reshape2_1.4.3 farver_2.0.1 uuid_0.1-2
[213] annotate_1.64.0 viridis_0.5.1 xml2_1.2.2 rvcheck_0.1.7
[217] AUCell_1.8.0 ggplotify_0.0.4 bit_1.1-14 jpeg_0.1-8.1
[221] spatstat.data_1.4-3 ggraph_2.0.0 pkgconfig_2.0.3 rvg_0.2.2
[225] knitr_1.26
Any advice would be appreciated.
Regards,
hanhuihong
dweemx commented
Hey @honghh2018 ,
Have you tried to use get_regulons(loom, attrName='Regulons') ?
dweemx commented
Closing issue since no activity