As.phylo as.treedata

[xiangpin]

Description

The original as.phylo and as.treedata can not convert the data.frame which contained the parent and children of tbl_tree.
They just supported converting the edge matrix of phylo class.

Related Issue

#59

Example

> library(treeio)
treeio v1.17.1.991  For help: https://yulab-smu.top/treedata-book/

If you use treeio in published research, please cite:

LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution 2020, 37(2):599-603. doi: 10.1093/molbev/msz240

> set.seed(2017)
> a <- rtree(4) %>% as_tibble() %>% as.data.frame()
> a
  parent node branch.length label
1      5    1   0.434905600    t4
2      7    2   0.674331481    t1
3      7    3   0.002020766    t3
4      6    4   0.025093514    t2
5      5    5            NA  <NA>
6      5    6   0.472166386  <NA>
7      6    7   0.273833123  <NA>
> class(a)
[1] "data.frame"
> a %>% as.treedata()
'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'.
> a %>% as.phylo(length="branch.length")

Phylogenetic tree with 4 tips and 3 internal nodes.

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

Rooted; includes branch lengths.
> a %>% as.treedata(length="branch.length")
'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; includes branch lengths.

with the following features available:
        'label'.