reroot tree problem

[liuqian666]

Describe you issue

Hello! I'm learning how to use ggtree according to treedata-Book, and here are the code: library(ggtree) library(treeio) library(tidytree) library(TDbook) trda <- tree_boots %>% left_join(df_tip_data, by=c("label" = "Newick_label")) %>% left_join(df_inode_data, by=c("label" = "newick_label")) trda trda2 <- root(trda, outgroup = "Suricata_suricatta", edgelabel = TRUE)

Then it shows: "Error in root.phylo(tree, outgroup = outgroup, node = node, edgelabel = edgelabel, : specified outgroup not in labels of the tree"

The packages are latest version. I've searched in google, and the problem still can't be solved. Hope for your reply. Thank you very much.

[xiangpin]

Which version of your treeio? How about updating treeio package? Please provide your R session information via sessionInfo().

[liuqian666]

Which version of your treeio? How about updating treeio package? Please provide your R session information via sessionInfo(). R version 4.1.1 (2021-08-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 [2] LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 [4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

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

other attached packages: [1] ggimage_0.3.0 aplot_0.1.2 phytools_1.0-1 maps_3.4.0 ape_5.6-1
[6] TDbook_0.0.5 ggplot2_3.3.5 tidytree_0.3.5 treeio_1.16.2 ggtree_3.0.4

loaded via a namespace (and not attached): [1] phangorn_2.8.1 tidyselect_1.1.2 purrr_0.3.4
[4] lattice_0.20-45 ggfun_0.0.5 colorspace_2.0-2
[7] vctrs_0.3.8 generics_0.1.2 expm_0.999-6
[10] viridisLite_0.4.0 utf8_1.2.2 gridGraphics_0.5-1
[13] rlang_1.0.1 pillar_1.7.0 withr_2.5.0
[16] glue_1.6.2 lifecycle_1.0.1 munsell_0.5.0
[19] combinat_0.0-8 gtable_0.3.0 codetools_0.2-18
[22] coda_0.19-4 labeling_0.4.2 parallel_4.1.1
[25] fansi_0.5.0 Rcpp_1.0.8 scales_1.1.1
[28] plotrix_3.8-2 clusterGeneration_1.3.7 magick_2.7.3
[31] scatterplot3d_0.3-41 jsonlite_1.8.0 tmvnsim_1.0-2
[34] farver_2.1.0 fastmatch_1.1-3 mnormt_2.0.2
[37] digest_0.6.29 dplyr_1.0.8 numDeriv_2016.8-1.1
[40] grid_4.1.1 quadprog_1.5-8 cli_3.2.0
[43] tools_4.1.1 yulab.utils_0.0.4 magrittr_2.0.1
[46] lazyeval_0.2.2 patchwork_1.1.1 tibble_3.1.5
[49] crayon_1.5.0 tidyr_1.1.4 pkgconfig_2.0.3
[52] ellipsis_0.3.2 MASS_7.3-55 Matrix_1.4-0
[55] ggnewscale_0.4.6 ggplotify_0.1.0 rstudioapi_0.13
[58] R6_2.5.1 igraph_1.2.11 nlme_3.1-153
[61] compiler_4.1.1

[liuqian666]

I can see the data of "trda" and plot it, but can't reroot any specified outgroup in this tree. Here 're the figure of this tree

[xiangpin]

I know, but your ggtree package suite is not the newest, the root function for treedata was updated in treeio (>=1.18.1). Please update the treeio package.

[liuqian666]

I know, but your ggtree package suite is not the newest, the root function for treedata was updated in treeio (>=1.18.1). Please update the treeio package.

Oh, I see, thank you very much! I was not very familiar with R, so I get confused with the version of packages. Thank you one more time!(^▽^)