tibble format: branch.length & label

[nick-youngblut]

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reprex

library(ape)
library(tidytree)
set.seed(2017)
tree <- rtree(4)
x <- as_tibble(as_tibble(tree))
as.treedata(x)

Output:

'treedata' S4 object'.

...@ phylo:

Phylogenetic tree with 4 tips and 3 internal nodes.

Tip labels:
  1, 4, 2, 3
Node labels:
  5, 6, 7

Rooted; no branch lengths.

with the following features available:
  'branch.length', 'label'.

# The associated data tibble abstraction: 7 × 4
# The 'node', 'label' and 'isTip' are from the phylo tree.
   node label.x isTip label.y
  <int> <chr>   <lgl> <chr>  
1     1 1       TRUE  t4     
2     2 4       TRUE  t2     
3     3 2       TRUE  t1     
4     4 3       TRUE  t3     
5     5 5       FALSE NA     
6     6 6       FALSE NA     
7     7 7       FALSE NA 

Description

If the as.treedata input is a tibble (or data.table) instead of a tbl_tree, neither branch.length nor label is recognized correctly. The function doc doesn't include info on how to deal with this formatting issue, which would be very helpful. There also seems to be no as_tbl_tree function for object conversion.

SessionInfo

R version 4.1.2 (2021-11-01)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS/LAPACK: /tmp/global2/nyoungblut/code/general/conda_envs/general-tidy-seq/lib/libopenblasp-r0.3.18.so

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

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

other attached packages:
[1] ape_5.6-2          ggtree_3.2.0       clustermq_0.8.95.3 LeyLabRMisc_0.2.1 
[5] tidytable_0.6.7    data.table_1.14.2  ggplot2_3.3.5      tidyr_1.2.0       
[9] dplyr_1.0.7       

loaded via a namespace (and not attached):
 [1] treeio_1.18.0      pbdZMQ_0.3-7       tidyselect_1.1.1   repr_1.1.4        
 [5] purrr_0.3.4        lattice_0.20-45    ggfun_0.0.5        colorspace_2.0-3  
 [9] vctrs_0.3.8        generics_0.1.2     htmltools_0.5.2    base64enc_0.1-3   
[13] utf8_1.2.2         gridGraphics_0.5-1 rlang_0.4.12       R.oo_1.24.0       
[17] pillar_1.7.0       glue_1.6.2         withr_2.5.0        R.utils_2.11.0    
[21] uuid_1.0-3         lifecycle_1.0.1    plyr_1.8.6         munsell_0.5.0     
[25] gtable_0.3.0       R.methodsS3_1.8.1  codetools_0.2-18   evaluate_0.15     
[29] labeling_0.4.2     fastmap_1.1.0      parallel_4.1.2     fansi_1.0.2       
[33] IRdisplay_1.1      Rcpp_1.0.8         scales_1.1.1       IRkernel_1.3      
[37] jsonlite_1.8.0     farver_2.1.0       digest_0.6.29      aplot_0.1.2       
[41] grid_4.1.2         cli_3.2.0          tools_4.1.2        yulab.utils_0.0.4 
[45] magrittr_2.0.2     lazyeval_0.2.2     patchwork_1.1.1    tibble_3.1.6      
[49] crayon_1.5.0       pkgconfig_2.0.3    tidytree_0.3.9     ellipsis_0.3.2    
[53] ggplotify_0.1.0    R6_2.5.1           nlme_3.1-155       compiler_4.1.2