clusterProfiler
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dotplot() error after compareCluster() for fun = "groupGO" with data(gcSample)
Describe your issue
Even using the example from the documentation I am getting errors:
> xx <- enrichplot::pairwise_termsim(xx)
> clusterProfiler::dotplot(xx)
> xx <- compareCluster(gcSample,
+ fun = "groupGO",
+ OrgDb= 'org.Hs.eg.db',
+ ont = "BP",
+ readable = TRUE)
> clusterProfiler::dotplot(xx)
Error in `geom_point()`:
! Problem while computing aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `compute_aesthetics()`:
! Aesthetics are not valid data columns.
✖ The following aesthetics are invalid:
✖ `colour = p.adjust`
ℹ Did you mistype the name of a data column or forget to add `after_stat()`?
Run `rlang::last_trace()` to see where the error occurred.
But enrichKEGG and enrichGO works as expected
data(gcSample)
xx <- compareCluster(gcSample, fun="enrichKEGG",
organism="hsa", pvalueCutoff=0.05)
xx <- enrichplot::pairwise_termsim(xx)
clusterProfiler::dotplot(xx)
Warning messages:
1: In utils::download.file(url, quiet = TRUE, method = method, ...) :
the 'wininet' method is deprecated for http:// and https:// URLs
2: In utils::download.file(url, quiet = TRUE, method = method, ...) :
the 'wininet' method is deprecated for http:// and https:// URLs
sessioninfo:
> sessionInfo()
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.utf8 LC_CTYPE=English_United Kingdom.utf8 LC_MONETARY=English_United Kingdom.utf8
[4] LC_NUMERIC=C LC_TIME=English_United Kingdom.utf8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0 GenomicFeatures_1.50.4
[3] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
[5] clusterProfiler_4.6.2 org.Mm.eg.db_3.16.0
[7] AnnotationDbi_1.60.2 IRanges_2.32.0
[9] S4Vectors_0.36.2 Biobase_2.58.0
[11] BiocGenerics_0.44.0
loaded via a namespace (and not attached):
[1] shadowtext_0.1.2 fastmatch_1.1-3 BiocFileCache_2.6.1 plyr_1.8.8
[5] igraph_1.4.2 lazyeval_0.2.2 splines_4.2.2 BiocParallel_1.32.6
[9] pathview_1.38.0 ggplot2_3.4.2 digest_0.6.31 yulab.utils_0.0.6
[13] GOSemSim_2.24.0 viridis_0.6.2 GO.db_3.16.0 fansi_1.0.4
[17] magrittr_2.0.3 memoise_2.0.1 Biostrings_2.66.0 graphlayouts_0.8.4
[21] matrixStats_0.63.0 enrichplot_1.18.3 prettyunits_1.1.1 colorspace_2.1-0
[25] blob_1.2.4 rappdirs_0.3.3 ggrepel_0.9.3 dplyr_1.1.2
[29] crayon_1.5.2 RCurl_1.98-1.12 jsonlite_1.8.4 graph_1.76.0
[33] scatterpie_0.1.8 ape_5.7-1 glue_1.6.2 polyclip_1.10-4
[37] gtable_0.3.3 zlibbioc_1.44.0 XVector_0.38.0 DelayedArray_0.24.0
[41] graphite_1.44.0 Rgraphviz_2.42.0 scales_1.2.1 DOSE_3.24.2
[45] futile.options_1.0.1 DBI_1.1.3 Rcpp_1.0.10 viridisLite_0.4.1
[49] progress_1.2.2 gridGraphics_0.5-1 tidytree_0.4.2 bit_4.0.5
[53] reactome.db_1.82.0 httr_1.4.5 fgsea_1.24.0 RColorBrewer_1.1-3
[57] pkgconfig_2.0.3 XML_3.99-0.14 farver_2.1.1 dbplyr_2.3.2
[61] utf8_1.2.3 ggplotify_0.1.0 tidyselect_1.2.0 labeling_0.4.2
[65] rlang_1.1.0 reshape2_1.4.4 munsell_0.5.0 tools_4.2.2
[69] cachem_1.0.7 downloader_0.4 cli_3.6.0 generics_0.1.3
[73] RSQLite_2.3.0 gson_0.1.0 stringr_1.5.0 fastmap_1.1.1
[77] yaml_2.3.7 ggtree_3.6.2 org.Hs.eg.db_3.16.0 bit64_4.0.5
[81] tidygraph_1.2.3 purrr_1.0.1 KEGGREST_1.38.0 ggraph_2.1.0
[85] ReactomePA_1.42.0 nlme_3.1-160 formatR_1.14 KEGGgraph_1.58.3
[89] aplot_0.1.10 xml2_1.3.3 biomaRt_2.54.1 compiler_4.2.2
[93] rstudioapi_0.14 filelock_1.0.2 curl_5.0.0 png_0.1-8
[97] treeio_1.22.0 tibble_3.2.1 tweenr_2.0.2 stringi_1.7.12
[101] futile.logger_1.4.3 lattice_0.21-8 Matrix_1.5-3 vctrs_0.6.0
[105] pillar_1.9.0 lifecycle_1.0.3 data.table_1.14.8 cowplot_1.1.1
[109] bitops_1.0-7 patchwork_1.1.2 rtracklayer_1.58.0 qvalue_2.30.0
[113] R6_2.5.1 BiocIO_1.8.0 gridExtra_2.3 codetools_0.2-18
[117] lambda.r_1.2.4 MASS_7.3-58.3 SummarizedExperiment_1.28.0 rjson_0.2.21
[121] withr_2.5.0 GenomicAlignments_1.34.1 Rsamtools_2.14.0 GenomeInfoDbData_1.2.9
[125] parallel_4.2.2 hms_1.1.3 VennDiagram_1.7.3 grid_4.2.2
[129] ggfun_0.0.9 tidyr_1.3.0 HDO.db_0.99.1 MatrixGenerics_1.10.0
[133] ggforce_0.4.1 restfulr_0.0.15