Entering edit mode
Francois Marchildon
▴
20
@francois-marchildon-14131
Last seen 2.1 years ago
Rockefeller University, New York City
Dear Bioconductor community,
I am trying to change the node text (something like geom_node_text
) with the emapplot function of the enrichplot package.
This is what I have unsuccessfully tried from an enrichResult object that is fine:
> ggoBP@result %>% names()
[1] "ID" "Description" "GeneRatio" "BgRatio" "pvalue"
[6] "p.adjust" "qvalue" "geneID" "Count"
> p <- emapplot(ggoBP, layout = "kk", line_scale = 0.2)
> p + geom_node_label(size = 9, repel = T)
Error: geom_label_repel requires the following missing aesthetics: label
Any suggestion would be welcome!
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
other attached packages:
[1] ggraph_2.0.3 circlize_0.4.10
[3] DOSE_3.14.0 msigdbr_7.1.1
[5] ggcorrplot_0.1.3 plyr_1.8.6
[7] tidyr_1.1.1 ReactomePA_1.32.0
[9] dplyr_1.0.1 ComplexHeatmap_2.4.3
[11] stringr_1.4.0 colorRamps_2.3
[13] VennDiagram_1.6.20 futile.logger_1.4.3
[15] clusterProfiler_3.16.0 reactome.db_1.70.0
[17] org.Mm.eg.db_3.11.4 AnnotationDbi_1.50.3
[19] ggrepel_0.8.2 gageData_2.26.0
[21] pathview_1.28.1 gage_2.38.3
[23] biomaRt_2.44.1 ggplot2_3.3.2
[25] pheatmap_1.0.12 RColorBrewer_1.1-2
[27] DESeq2_1.28.1 SummarizedExperiment_1.18.2
[29] DelayedArray_0.14.1 matrixStats_0.56.0
[31] Biobase_2.48.0 GenomicRanges_1.40.0
[33] GenomeInfoDb_1.24.2 IRanges_2.22.2
[35] S4Vectors_0.26.1 BiocGenerics_0.34.0
loaded via a namespace (and not attached):
[1] backports_1.1.8 fastmatch_1.1-0 BiocFileCache_1.12.0
[4] igraph_1.2.5 splines_4.0.2 BiocParallel_1.22.0
[7] urltools_1.7.3 digest_0.6.25 GOSemSim_2.14.1
[10] viridis_0.5.1 GO.db_3.11.4 checkmate_2.0.0
[13] magrittr_1.5 memoise_1.1.0 cluster_2.1.0
[16] Biostrings_2.56.0 annotate_1.66.0 graphlayouts_0.7.0
[19] askpass_1.1 enrichplot_1.8.1 prettyunits_1.1.1
[22] colorspace_1.4-1 blob_1.2.1 rappdirs_0.3.1
[25] xfun_0.16 crayon_1.3.4 RCurl_1.98-1.2
[28] jsonlite_1.7.0 graph_1.66.0 scatterpie_0.1.4
[31] genefilter_1.70.0 survival_3.2-3 glue_1.4.1
[34] polyclip_1.10-0 gtable_0.3.0 zlibbioc_1.34.0
[37] XVector_0.28.0 GetoptLong_1.0.2 graphite_1.34.0
[40] Rgraphviz_2.32.0 shape_1.4.4 scales_1.1.1
[43] futile.options_1.0.1 DBI_1.1.0 Rcpp_1.0.5
[46] viridisLite_0.3.0 xtable_1.8-4 progress_1.2.2
[49] clue_0.3-57 gridGraphics_0.5-0 bit_4.0.3
[52] europepmc_0.4 httr_1.4.2 fgsea_1.14.0
[55] ellipsis_0.3.1 pkgconfig_2.0.3 XML_3.99-0.5
[58] farver_2.0.3 dbplyr_1.4.4 locfit_1.5-9.4
[61] ggplotify_0.0.5 tidyselect_1.1.0 rlang_0.4.7
[64] reshape2_1.4.4 munsell_0.5.0 tools_4.0.2
[67] downloader_0.4 generics_0.0.2 RSQLite_2.2.0
[70] ggridges_0.5.2 org.Hs.eg.db_3.11.4 bit64_4.0.2
[73] tidygraph_1.2.0 purrr_0.3.4 KEGGREST_1.28.0
[76] formatR_1.7 KEGGgraph_1.48.0 DO.db_2.9
[79] xml2_1.3.2 compiler_4.0.2 rstudioapi_0.11
[82] curl_4.3 png_0.1-7 tibble_3.0.3
[85] tweenr_1.0.1 geneplotter_1.66.0 stringi_1.4.6
[88] lattice_0.20-41 Matrix_1.2-18 vctrs_0.3.2
[91] pillar_1.4.6 lifecycle_0.2.0 BiocManager_1.30.10
[94] triebeard_0.3.0 GlobalOptions_0.1.2 data.table_1.13.0
[97] cowplot_1.0.0 bitops_1.0-6 qvalue_2.20.0
[100] R6_2.4.1 gridExtra_2.3 lambda.r_1.2.4
[103] MASS_7.3-51.6 assertthat_0.2.1 rjson_0.2.20
[106] openssl_1.4.2 withr_2.2.0 GenomeInfoDbData_1.2.3
[109] hms_0.5.3 rvcheck_0.1.8 ggforce_0.3.2
[112] tinytex_0.25
Just curious: Why is
enrichPlot
not on yoursessionInfo()
output?Also, you might want to edit your post and add code formatting so
geom_node_text
doesn't show up as geomnodetext - markdown turns the underscores into markers for italicization.