Entering edit mode
17 months ago
Pahi
▴
20
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
I met the same error. Do you have a solution for this problem?