why does my treeplot only appear partially?

[chansigit]

like this?

[chansigit]

R version 4.1.1 (2021-08-10) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 20.04.6 LTS

Matrix products: default BLAS/LAPACK: /home/csj/anaconda3/envs/r411py37/lib/libopenblasp-r0.3.17.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=zh_CN.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=zh_CN.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=zh_CN.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=zh_CN.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] GOSemSim_2.18.1 tidytree_0.4.2 enrichplot_1.12.3
[4] ggnewscale_0.4.9 dittoSeq_1.4.4 ggplot2_3.4.3
[7] clusterProfiler_4.0.5 dplyr_1.1.4 tidyseurat_0.7.2
[10] ttservice_0.3.8 SeuratObject_4.1.3 Seurat_4.3.0.1
[13] reticulate_1.31

loaded via a namespace (and not attached): [1] utf8_1.2.4 spatstat.explore_3.2-3
[3] tidyselect_1.2.0 RSQLite_2.3.1
[5] AnnotationDbi_1.54.1 htmlwidgets_1.6.2
[7] grid_4.1.1 BiocParallel_1.26.2
[9] Rtsne_0.16 scatterpie_0.2.1
[11] munsell_0.5.0 codetools_0.2-19
[13] ica_1.0-3 pbdZMQ_0.3-10
[15] future_1.33.0 miniUI_0.1.1.1
[17] withr_2.5.2 spatstat.random_3.1-6
[19] colorspace_2.1-0 progressr_0.14.0
[21] Biobase_2.52.0 uuid_1.1-1
[23] stats4_4.1.1 SingleCellExperiment_1.14.1 [25] ROCR_1.0-11 tensor_1.5
[27] DOSE_3.18.3 listenv_0.9.0
[29] labeling_0.4.3 MatrixGenerics_1.4.3
[31] repr_1.1.6 GenomeInfoDbData_1.2.6
[33] polyclip_1.10-4 pheatmap_1.0.12
[35] bit64_4.0.5 farver_2.1.1
[37] downloader_0.4 parallelly_1.36.0
[39] vctrs_0.6.5 treeio_1.16.2
[41] generics_0.1.3 R6_2.5.1
[43] GenomeInfoDb_1.28.4 ggVolcano_0.0.2
[45] graphlayouts_1.0.0 DelayedArray_0.18.0
[47] bitops_1.0-7 spatstat.utils_3.0-3
[49] cachem_1.0.8 fgsea_1.18.0
[51] gridGraphics_0.5-1 promises_1.2.1
[53] scales_1.2.1 ggraph_2.1.0
[55] gtable_0.3.4 Cairo_1.6-1
[57] globals_0.16.2 goftest_1.2-3
[59] tidygraph_1.2.3 rlang_1.1.2
[61] splines_4.1.1 lazyeval_0.2.2
[63] spatstat.geom_3.2-5 reshape2_1.4.4
[65] abind_1.4-5 httpuv_1.6.11
[67] qvalue_2.24.0 tools_4.1.1
[69] ggplotify_0.1.2 ellipsis_0.3.2
[71] RColorBrewer_1.1-3 BiocGenerics_0.38.0
[73] ggridges_0.5.4 latex2exp_0.9.6
[75] Rcpp_1.0.11 plyr_1.8.8
[77] base64enc_0.1-3 zlibbioc_1.38.0
[79] purrr_1.0.2 RCurl_1.98-1.12
[81] deldir_1.0-9 pbapply_1.7-2
[83] viridis_0.6.4 cowplot_1.1.1
[85] S4Vectors_0.30.2 zoo_1.8-12
[87] SummarizedExperiment_1.22.0 ggrepel_0.9.3
[89] cluster_2.1.4 fs_1.6.3
[91] magrittr_2.0.3 data.table_1.14.8
[93] scattermore_1.2 DO.db_2.9
[95] lmtest_0.9-40 RANN_2.6.1
[97] fitdistrplus_1.1-11 matrixStats_1.0.0
[99] patchwork_1.1.3 mime_0.12
[101] evaluate_0.21 xtable_1.8-4
[103] IRanges_2.26.0 gridExtra_2.3
[105] compiler_4.1.1 tibble_3.2.1
[107] KernSmooth_2.23-22 crayon_1.5.2
[109] shadowtext_0.1.2 htmltools_0.5.6
[111] ggfun_0.1.2 later_1.3.1
[113] tidyr_1.3.0 aplot_0.2.0
[115] DBI_1.1.3 tweenr_2.0.2
[117] MASS_7.3-60 Matrix_1.6-1
[119] cli_3.6.1 parallel_4.1.1
[121] igraph_1.5.1 GenomicRanges_1.44.0
[123] pkgconfig_2.0.3 sp_2.0-0
[125] IRdisplay_1.1 plotly_4.10.2
[127] spatstat.sparse_3.0-2 ggtree_3.7.1.002
[129] XVector_0.32.0 yulab.utils_0.1.0
[131] stringr_1.5.1 digest_0.6.33
[133] sctransform_0.3.5 RcppAnnoy_0.0.20
[135] spatstat.data_3.0-1 Biostrings_2.60.2
[137] leiden_0.4.3 fastmatch_1.1-4
[139] uwot_0.1.16 shiny_1.7.5
[141] lifecycle_1.0.4 nlme_3.1-163
[143] jsonlite_1.8.7 viridisLite_0.4.2
[145] fansi_1.0.5 pillar_1.9.0
[147] lattice_0.21-8 KEGGREST_1.32.0
[149] fastmap_1.1.1 httr_1.4.7
[151] survival_3.5-7 GO.db_3.13.0
[153] glue_1.6.2 png_0.1-8
[155] bit_4.0.5 ggforce_0.4.1
[157] stringi_1.7.3 blob_1.2.4
[159] memoise_2.0.1 IRkernel_1.3.2
[161] tidyverse_2.0.0 irlba_2.3.5.1
[163] future.apply_1.11.0 ape_5.7-1

[guidohooiveld]

Please show the exact code on how ego2 was generated.

Did you also notice the warning on the use of 'label'?

Also note that you are using an old version of R (and corresponding Bioconductor packages); these are more than 2 years old! Please use the latest version of R (=R-4.3.x) and Bioconductor (=3.18) since development of packages goes on continuously!