Deleted:treeplot error: Error in offspring.tbl_tree_item(.data = .data, .node = .node, tiponly = tiponly, : could not find function "offspring.tbl_tree_item"
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@d4a334e3
Last seen 13 months ago
Germany

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
pairwise clusterProfiler treeplot • 1.7k views
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