clusterProfiler
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Published
20 hours ago •
YuLab-SMU
YuLab-SMU
goplot no longer works with clusterProfiler 4.12.3
Prerequisites
- [x] Have you read Feedback and followed the guide?
- [x] make sure you are using the latest release version
- [x] read the documentation
- [x] google your quesion/issue
Describe your issue
- [x] Make a reproducible example (e.g. 1)
- [x] your code should contain comments to describe the problem (e.g. what you expected and what actually happened)
I can get around the installation problem if I manually install the latest version of yulab.utils.
This works using Docker and the image rocker/verse:4.4.0.
install.packages("remotes")
remotes::install_version("yulab.utils", version = "0.1.6", repos = "https://cloud.r-project.org/")
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("clusterProfiler")
But then goplot() no longer works in clusterProfiler 4.12.3. Using the example from the documentation:
library(clusterProfiler)
data(geneList, package = "DOSE")
de <- names(geneList)[1:100]
yy <- enrichGO(de, 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)
goplot(yy)
Error in AnnotationDbi::mget(id, GOANCESTOR) :
second argument must be an environment
Session info.
sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] clusterProfiler_4.12.3 BiocManager_1.30.23 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8 magrittr_2.0.3
[5] farver_2.1.2 rmarkdown_2.27 fs_1.6.4 zlibbioc_1.50.0
[9] vctrs_0.6.5 memoise_2.0.1 ggtree_3.12.0 htmltools_0.5.8.1
[13] AnnotationHub_3.12.0 curl_5.2.1 gridGraphics_0.5-1 plyr_1.8.9
[17] httr2_1.0.2 cachem_1.1.0 whisker_0.4.1 igraph_2.0.3
[21] lifecycle_1.0.4 pkgconfig_2.0.3 gson_0.1.0 Matrix_1.7-0
[25] R6_2.5.1 fastmap_1.2.0 GenomeInfoDbData_1.2.12 digest_0.6.35
[29] aplot_0.2.2 enrichplot_1.24.2 colorspace_2.1-0 patchwork_1.2.0
[33] AnnotationDbi_1.66.0 S4Vectors_0.42.1 ps_1.7.6 rprojroot_2.0.4
[37] RSQLite_2.3.7 org.Hs.eg.db_3.19.1 filelock_1.0.3 fansi_1.0.6
[41] httr_1.4.7 polyclip_1.10-6 compiler_4.4.0 remotes_2.5.0
[45] bit64_4.0.5 withr_3.0.1 BiocParallel_1.38.0 viridis_0.6.5
[49] DBI_1.2.3 ggforce_0.4.2 MASS_7.3-60.2 rappdirs_0.3.3
[53] HDO.db_0.99.1 tools_4.4.0 scatterpie_0.2.3 ape_5.8
[57] httpuv_1.6.15 glue_1.7.0 callr_3.7.6 nlme_3.1-164
[61] GOSemSim_2.30.1 promises_1.3.0 shadowtext_0.1.3 grid_4.4.0
[65] getPass_0.2-4 reshape2_1.4.4 fgsea_1.30.0 generics_0.1.3
[69] gtable_0.3.5 tidyr_1.3.1 data.table_1.15.4 tidygraph_1.3.1
[73] utf8_1.2.4 XVector_0.44.0 BiocGenerics_0.50.0 ggrepel_0.9.5
[77] BiocVersion_3.19.1 pillar_1.9.0 stringr_1.5.1 yulab.utils_0.1.6
[81] later_1.3.2 splines_4.4.0 dplyr_1.1.4 tweenr_2.0.3
[85] treeio_1.28.0 BiocFileCache_2.12.0 lattice_0.22-6 bit_4.0.5
[89] tidyselect_1.2.1 GO.db_3.19.1 Biostrings_2.72.1 knitr_1.47
[93] git2r_0.33.0 gridExtra_2.3 IRanges_2.38.1 stats4_4.4.0
[97] xfun_0.44 graphlayouts_1.1.1 Biobase_2.64.0 stringi_1.8.4
[101] UCSC.utils_1.0.0 lazyeval_0.2.2 ggfun_0.1.5 yaml_2.3.8
[105] evaluate_0.24.0 codetools_0.2-20 ggraph_2.2.1 tibble_3.2.1
[109] qvalue_2.36.0 ggplotify_0.1.2 cli_3.6.2 munsell_0.5.1
[113] processx_3.8.4 Rcpp_1.0.12 GenomeInfoDb_1.40.1 dbplyr_2.5.0
[117] png_0.1-8 parallel_4.4.0 ggplot2_3.5.1 blob_1.2.4
[121] DOSE_3.30.2 viridisLite_0.4.2 tidytree_0.4.6 scales_1.3.0
[125] purrr_1.0.2 crayon_1.5.2 rlang_1.1.4 cowplot_1.1.3
[129] fastmatch_1.1-4 KEGGREST_1.44.1
Ask in the right place
- [x] for bugs or feature requests, post here (github issue)
- [ ] for questions, please post to Bioconductor or Biostars with the tag
clusterProfiler
FWIW: it is working in my hands.... !?
> library(clusterProfiler)
> data(geneList, package = "DOSE")
> de <- names(geneList)[1:100]
> yy <- enrichGO(de, 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)
> goplot(yy)
>
> BiocManager::valid()
[1] TRUE
>
> packageVersion("yulab.utils")
[1] ‘0.1.6’
> packageVersion("clusterProfiler")
[1] ‘4.12.3’
> packageVersion("enrichplot")
[1] ‘1.24.2’
> packageVersion("GOSemSim")
[1] ‘2.30.1’
>
> R.Version()$version.string
[1] "R version 4.4.0 Patched (2024-05-21 r86580 ucrt)"
>
> sessionInfo()
R version 4.4.0 Patched (2024-05-21 r86580 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: Europe/Amsterdam
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] clusterProfiler_4.12.3
loaded via a namespace (and not attached):
[1] DBI_1.2.3 gson_0.1.0 shadowtext_0.1.4
[4] gridExtra_2.3 httr2_1.0.2 rlang_1.1.4
[7] magrittr_2.0.3 DOSE_3.30.2 compiler_4.4.0
[10] RSQLite_2.3.7 png_0.1-8 vctrs_0.6.5
[13] reshape2_1.4.4 stringr_1.5.1 pkgconfig_2.0.3
[16] crayon_1.5.3 fastmap_1.2.0 XVector_0.44.0
[19] labeling_0.4.3 ggraph_2.2.1 utf8_1.2.4
[22] HDO.db_0.99.1 enrichplot_1.24.2 UCSC.utils_1.0.0
[25] purrr_1.0.2 bit_4.0.5 zlibbioc_1.50.0
[28] cachem_1.1.0 aplot_0.2.3 GenomeInfoDb_1.40.1
[31] jsonlite_1.8.8 blob_1.2.4 BiocParallel_1.38.0
[34] tweenr_2.0.3 parallel_4.4.0 R6_2.5.1
[37] stringi_1.8.4 RColorBrewer_1.1-3 GOSemSim_2.30.1
[40] Rcpp_1.0.13 IRanges_2.38.1 Matrix_1.7-0
[43] splines_4.4.0 igraph_2.0.3 tidyselect_1.2.1
[46] qvalue_2.36.0 viridis_0.6.5 codetools_0.2-20
[49] lattice_0.22-6 tibble_3.2.1 plyr_1.8.9
[52] Biobase_2.64.0 treeio_1.28.0 withr_3.0.1
[55] KEGGREST_1.44.1 gridGraphics_0.5-1 scatterpie_0.2.3
[58] polyclip_1.10-7 Biostrings_2.72.1 pillar_1.9.0
[61] ggtree_3.12.0 stats4_4.4.0 ggfun_0.1.5
[64] generics_0.1.3 S4Vectors_0.42.1 ggplot2_3.5.1
[67] munsell_0.5.1 scales_1.3.0 tidytree_0.4.6
[70] glue_1.7.0 lazyeval_0.2.2 tools_4.4.0
[73] data.table_1.15.4 fgsea_1.30.0 fs_1.6.4
[76] graphlayouts_1.1.1 fastmatch_1.1-4 tidygraph_1.3.1
[79] cowplot_1.1.3 grid_4.4.0 tidyr_1.3.1
[82] ape_5.8 AnnotationDbi_1.66.0 colorspace_2.1-1
[85] nlme_3.1-166 GenomeInfoDbData_1.2.12 patchwork_1.2.0
[88] ggforce_0.4.2 cli_3.6.3 rappdirs_0.3.3
[91] fansi_1.0.6 viridisLite_0.4.2 dplyr_1.1.4
[94] gtable_0.3.5 yulab.utils_0.1.6 digest_0.6.37
[97] BiocGenerics_0.50.0 ggrepel_0.9.5 ggplotify_0.1.2
[100] org.Hs.eg.db_3.19.1 farver_2.1.2 memoise_2.0.1
[103] lifecycle_1.0.4 httr_1.4.7 GO.db_3.19.1
[106] bit64_4.0.5 MASS_7.3-61
>
