Enrichplot - goplot error
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Entering edit mode
9 weeks ago
Pahi ▴ 10

Hi!

I use enrichplot's goplot to visualise my enrichment results. I built a code for that and until this day everything was working. But today when I ran my code I got an error when it reaches goplot.

My enrichment result:

# over-representation test
#
#...@organism    Homo sapiens 
#...@ontology    GOALL 
#...@keytype     ENSEMBL 
#...@gene    chr [1:443] "ENSG00000142611" "ENSG00000269896" "ENSG00000162494" "ENSG00000066056" "ENSG00000162595" "ENSG00000184588" "ENSG00000116774" ...
#...pvalues adjusted by 'BH' with cutoff <0.05 
#...22 enriched terms found
'data.frame':   22 obs. of  10 variables:
 $ ONTOLOGY   : chr  "CC" "CC" "CC" "CC" ...
 $ ID         : chr  "GO:0045095" "GO:0030312" "GO:0031012" "GO:0098797" ...
 $ Description: chr  "keratin filament" "external encapsulating structure" "extracellular matrix" "plasma membrane protein complex" ...
 $ GeneRatio  : chr  "6/345" "23/345" "23/345" "23/345" ...
 $ BgRatio    : chr  "21/13183" "366/13183" "366/13183" "366/13183" ...
 $ pvalue     : num  1.20e-05 9.71e-05 9.71e-05 9.71e-05 2.79e-04 ...
 $ p.adjust   : num  0.00395 0.00801 0.00801 0.00801 0.01563 ...
 $ qvalue     : num  0.00369 0.00748 0.00748 0.00748 0.01461 ...
 $ geneID     : chr  "KRT6B/KRT4/KRT83/KRT71/KRT7/KRTAP2-3" "CHI3L1/HMCN1/S100A4/LTBP1/LRRTM4/LRRN1/BMPER/BGN/SCARA3/TNFRSF11B/MMP7/MMP13/ADAMTS14/ANXA8/A2M/SERPINA1/GREM1/"| __truncated__ "CHI3L1/HMCN1/S100A4/LTBP1/LRRTM4/LRRN1/BMPER/BGN/SCARA3/TNFRSF11B/MMP7/MMP13/ADAMTS14/ANXA8/A2M/SERPINA1/GREM1/"| __truncated__ "LRRC38/PDE4B/CNIH3/DPP10/SCN3A/CTNNA2/IL18R1/SCN2A/KCNIP4/C7/HCN1/SGCD/PLP1/SGCZ/KCNB2/TRAF1/CD3D/SSPN/CDH5/CDH"| __truncated__ ...
 $ Count      : int  6 23 23 23 8 18 8 10 6 15 ...
#...Citation
 T Wu, E Hu, S Xu, M Chen, P Guo, Z Dai, T Feng, L Zhou, W Tang, L Zhan, X Fu, S Liu, X Bo, and G Yu.
 clusterProfiler 4.0: A universal enrichment tool for interpreting omics data.
 The Innovation. 2021, 2(3):100141 

When I call goplot:

>a <- goplot(bp_data, showCategory = 10)
>?

This appears. And no matter what I write here, R session crashes or I get an error message. For example if I write bp_data again after the?, I get this message:

  Error in AnnotationDbi::mget(id, GOANCESTOR) : 
  second argument must be an environment

And as I said before it was working no problem.

Thank you for your help in advance!

My session info:

    R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=Hungarian_Hungary.1250  LC_CTYPE=Hungarian_Hungary.1250    LC_MONETARY=Hungarian_Hungary.1250 LC_NUMERIC=C                      
[5] LC_TIME=Hungarian_Hungary.1250    

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.5.1               purrr_0.3.4                 readr_2.1.2                 tidyr_1.1.4                 tibble_3.1.5               
 [6] tidyverse_1.3.2             ggpubr_0.4.0                stringr_1.4.0               ReactomePA_1.38.0           scales_1.1.1               
[11] rockchalk_1.8.151           kableExtra_1.3.4            gridExtra_2.3               patchwork_1.1.1             fuzzySim_4.8.1             
[16] dplyr_1.0.7                 pathview_1.34.0             DEFormats_1.22.0            DT_0.25                     knitr_1.40                 
[21] topGO_2.46.0                SparseM_1.81                GO.db_3.14.0                graph_1.72.0                pheatmap_1.0.12            
[26] openxlsx_4.2.5              RColorBrewer_1.1-3          gplots_3.1.3                Glimma_2.4.0                DESeq2_1.33.5              
[31] SummarizedExperiment_1.24.0 MatrixGenerics_1.6.0        matrixStats_0.61.0          GenomicRanges_1.45.0        GenomeInfoDb_1.29.8        
[36] DOSE_3.20.1                 ggridges_0.5.3              ggnewscale_0.4.7            enrichplot_1.14.1           ggplot2_3.3.6              
[41] clusterProfiler_4.2.2       org.Dm.eg.db_3.14.0         org.Hs.eg.db_3.14.0         AnnotationDbi_1.55.1        IRanges_2.27.2             
[46] S4Vectors_0.31.5            Biobase_2.53.0              BiocGenerics_0.39.2         edgeR_3.36.0                limma_3.49.4               
[51] rnaseq.pmb_0.1.0           

loaded via a namespace (and not attached):
  [1] rappdirs_0.3.3         bit64_4.0.5            DelayedArray_0.19.4    data.table_1.14.2      KEGGREST_1.34.0        RCurl_1.98-1.5        
  [7] generics_0.1.2         callr_3.7.0            usethis_2.1.5          RSQLite_2.2.8          shadowtext_0.1.2       tzdb_0.3.0            
 [13] bit_4.0.4              webshot_0.5.3          xml2_1.3.3             lubridate_1.8.0        assertthat_0.2.1       viridis_0.6.2         
 [19] gargle_1.2.0           xfun_0.29              hms_1.1.1              evaluate_0.15          fansi_0.5.0            readxl_1.4.0          
 [25] caTools_1.18.2         dbplyr_2.1.1           Rgraphviz_2.38.0       igraph_1.2.6           DBI_1.1.2              geneplotter_1.72.0    
 [31] htmlwidgets_1.5.4      googledrive_2.0.0      ellipsis_0.3.2         backports_1.4.1        annotate_1.72.0        vctrs_0.3.8           
 [37] remotes_2.4.2          abind_1.4-5            cachem_1.0.6           withr_2.5.0            ggforce_0.3.3          checkmate_2.0.0       
 [43] treeio_1.18.1          prettyunits_1.1.1      svglite_2.0.0          ape_5.5                lazyeval_0.2.2         crayon_1.5.1          
 [49] genefilter_1.75.1      labeling_0.4.2         pkgconfig_2.0.3        tweenr_1.0.2           nlme_3.1-153           pkgload_1.2.4         
 [55] devtools_2.4.3         rlang_1.0.2            lifecycle_1.0.1        downloader_0.4         kutils_1.70            modelr_0.1.8          
 [61] cellranger_1.1.0       rprojroot_2.0.3        polyclip_1.10-0        Matrix_1.3-4           aplot_0.1.3            carData_3.0-5         
 [67] boot_1.3-28            reprex_2.0.1           processx_3.5.2         googlesheets4_1.0.0    png_0.1-7              viridisLite_0.4.0     
 [73] bitops_1.0-7           KernSmooth_2.23-20     Biostrings_2.61.2      blob_1.2.3             qvalue_2.26.0          rstatix_0.7.0         
 [79] gridGraphics_0.5-1     ggsignif_0.6.3         reactome.db_1.77.0     memoise_2.0.1          graphite_1.40.0        magrittr_2.0.1        
 [85] plyr_1.8.6             zlibbioc_1.39.0        compiler_4.1.1         scatterpie_0.1.7       KEGGgraph_1.54.0       lme4_1.1-27.1         
 [91] cli_3.1.1              XVector_0.33.0         ps_1.6.0               MASS_7.3-54            tidyselect_1.1.2       stringi_1.7.5         
 [97] ggupset_0.3.0          yaml_2.2.1             GOSemSim_2.19.1        locfit_1.5-9.4         ggrepel_0.9.1          grid_4.1.1            
[103] fastmatch_1.1-3        tools_4.1.1            parallel_4.1.1         rstudioapi_0.13        foreign_0.8-81         farver_2.1.0          
[109] ggraph_2.0.5           digest_0.6.28          Rcpp_1.0.7             car_3.0-13             broom_0.8.0            httr_1.4.3            
[115] modEvA_3.0             colorspace_2.0-2       rvest_1.0.2            brio_1.1.3             XML_3.99-0.8           fs_1.5.2              
[121] splines_4.1.1          yulab.utils_0.0.4      tidytree_0.3.9         graphlayouts_0.7.1     ggplotify_0.1.0        sessioninfo_1.2.2     
[127] systemfonts_1.0.3      xtable_1.8-4           jsonlite_1.7.2         nloptr_2.0.0           ggtree_3.2.1           tidygraph_1.2.0       
[133] ggfun_0.0.6            testthat_3.1.2         R6_2.5.1               pillar_1.7.0           htmltools_0.5.2        glue_1.4.2            
[139] fastmap_1.1.0          minqa_1.2.4            BiocParallel_1.27.16   fgsea_1.19.4           pkgbuild_1.3.1         utf8_1.2.2            
[145] lattice_0.20-45        gtools_3.9.2           zip_2.2.0              survival_3.2-13        rmarkdown_2.14         desc_1.4.1            
[151] munsell_0.5.0          DO.db_2.9              GenomeInfoDbData_1.2.7 haven_2.5.0            reshape2_1.4.4         gtable_0.3.0 
enrichplot r goplot • 148 views
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