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aertslab / SCopeLoomR

R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...
MIT License
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why the SCopeLoomR showing not get_regulons function #23

Closed honghh2018 closed 4 years ago

honghh2018 commented 4 years ago

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: image Best, hanhuihong

honghh2018 commented 4 years ago

Hi @All, This question had solved with the ScopeLoomR package compiled with higher version h5cc. Thanks

honghh2018 commented 4 years ago

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 4 years ago

Hey @honghh2018 ,

Have you tried to use get_regulons(loom, attrName='Regulons') ?

dweemx commented 4 years ago

Closing issue since no activity