Entering edit mode
Hello! I am doing Bulk RNAseq analysis and would like to cluster the results of the GO enrichment analysis in a tree and I have been facing this error
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned. Error in offspring.tbl_tree_item(.data = .data, .node = .node, tiponly = tiponly, : could not find function "offspring.tbl_tree_item"
could you please help where I missed somtheing? I managed to plot the ego in dotplot so there should be no problem before that step.
Best
Ruba
ego <- enrichGO(gene = KeggSegGen.1,
universe = universe,
OrgDb = org.Mm.eg.db,
keyType = "ENSEMBL",
ont = "BP",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
readable = TRUE)
ego.1 <- ego %>% top_n(50, wt=-p.adjust)
egox <- setReadable(ego.1, 'org.Mm.eg.db', 'ENTREZID')
egox2 <- pairwise_termsim(egox)
treeplot(egox2)
#output
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
Error in offspring.tbl_tree_item(.data = .data, .node = .node, tiponly = tiponly, :
could not find function "offspring.tbl_tree_item"
> sessionInfo( )
R version 4.2.3 (2023-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 11 (bullseye)
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-r0.3.13.so
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
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DOSE_3.24.2 GOSemSim_2.24.0 enrichplot_1.18.4 igraph_1.4.1
[5] KEGGgraph_1.58.3 pathview_1.38.0 org.Mm.eg.db_3.16.0 AnnotationDbi_1.60.2
[9] clusterProfiler_4.9.0 EnhancedVolcano_1.16.0 ggrepel_0.9.3 ashr_2.2-63
[13] biomaRt_2.54.1 tximport_1.26.1 lubridate_1.9.2 forcats_1.0.0
[17] stringr_1.5.0 dplyr_1.1.0 purrr_1.0.1 readr_2.1.4
[21] tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.1 tidyverse_2.0.0
[25] DESeq2_1.38.3 SummarizedExperiment_1.28.0 Biobase_2.58.0 MatrixGenerics_1.10.0
[29] matrixStats_0.63.0 GenomicRanges_1.50.2 GenomeInfoDb_1.34.9 IRanges_2.32.0
[33] S4Vectors_0.36.2 BiocGenerics_0.44.0 BiocManager_1.30.22
loaded via a namespace (and not attached):
[1] utf8_1.2.3 tidyselect_1.2.0 RSQLite_2.3.0 htmlwidgets_1.6.2 grid_4.2.3
[6] BiocParallel_1.30.4 devtools_2.4.5 scatterpie_0.2.1 munsell_0.5.0 codetools_0.2-19
[11] miniUI_0.1.1.1 withr_2.5.0 colorspace_2.1-0 filelock_1.0.2 rstudioapi_0.15.0
[16] labeling_0.4.2 GenomeInfoDbData_1.2.9 mixsqp_0.3-48 polyclip_1.10-4 bit64_4.0.5
[21] farver_2.1.1 downloader_0.4 vctrs_0.5.2 treeio_1.22.0 generics_0.1.3
[26] gson_0.1.0 timechange_0.2.0 BiocFileCache_2.6.1 R6_2.5.1 graphlayouts_0.8.4
[31] invgamma_1.1 locfit_1.5-9.7 bitops_1.0-7 cachem_1.0.7 fgsea_1.24.0
[36] gridGraphics_0.5-1 DelayedArray_0.24.0 promises_1.2.1 scales_1.2.1 vroom_1.6.3
[41] ggraph_2.1.0 gtable_0.3.1 processx_3.8.0 tidygraph_1.2.3 rlang_1.0.6
[46] splines_4.2.3 lazyeval_0.2.2 reshape2_1.4.4 httpuv_1.6.9 qvalue_2.30.0
[51] tools_4.2.3 usethis_2.1.6 ggplotify_0.1.2 ellipsis_0.3.2 RColorBrewer_1.1-3
[56] sessioninfo_1.2.2 Rcpp_1.0.10 plyr_1.8.8 progress_1.2.2 zlibbioc_1.44.0
[61] RCurl_1.98-1.10 ps_1.7.2 prettyunits_1.1.1 viridis_0.6.4 cowplot_1.1.1
[66] urlchecker_1.0.1 fs_1.6.1 magrittr_2.0.3 data.table_1.14.8 truncnorm_1.0-9
[71] SQUAREM_2021.1 ggnewscale_0.4.9 pkgload_1.3.2.1 hms_1.1.3 patchwork_1.1.3
[76] mime_0.12 xtable_1.8-4 HDO.db_0.99.1 XML_3.99-0.13 gridExtra_2.3
[81] compiler_4.2.3 crayon_1.5.2 shadowtext_0.1.2 htmltools_0.5.4 ggfun_0.1.2
[86] later_1.3.1 tzdb_0.4.0 geneplotter_1.76.0 aplot_0.2.0 DBI_1.1.3
[91] tweenr_2.0.2 dbplyr_2.3.3 MASS_7.3-60 rappdirs_0.3.3 Matrix_1.6-1
[96] cli_3.6.0 parallel_4.2.3 pkgconfig_2.0.3 xml2_1.3.5 ggtree_3.6.2
[101] annotate_1.76.0 XVector_0.38.0 yulab.utils_0.0.8 callr_3.7.3 digest_0.6.31
[106] graph_1.76.0 Biostrings_2.66.0 fastmatch_1.1-4 tidytree_0.4.5 curl_5.0.0
[111] shiny_1.7.5 lifecycle_1.0.3 nlme_3.1-162 jsonlite_1.8.4 viridisLite_0.4.2
[116] fansi_1.0.4 pillar_1.9.0 lattice_0.21-8 KEGGREST_1.41.0 fastmap_1.1.1
[121] httr_1.4.7 pkgbuild_1.4.2 GO.db_3.16.0 glue_1.6.2 remotes_2.4.2.1
[126] png_0.1-8 bit_4.0.5 Rgraphviz_2.42.0 ggforce_0.4.1 stringi_1.7.12
[131] profvis_0.3.8 blob_1.2.4 org.Hs.eg.db_3.16.0 memoise_2.0.1 irlba_2.3.5.1
[136] ape_5.7