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YuLab-SMU / treeio

:seedling: Base Classes and Functions for Phylogenetic Tree Input and Output
https://yulab-smu.top/treedata-book/
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add write.jplace #115

Closed xiangpin closed 9 months ago

xiangpin commented 11 months ago

Description

add write.jplace function to write the jplace clas to file.

Related Issue

https://github.com/YuLab-SMU/treeio/issues/112

Example

> jp <- system.file("extdata", "sample.jplace", package="treeio")

> tr1 <- read.jplace(jp)

> outfile <- tempfile()

> write.jplace(tr1, outfile)

> tr2 <- read.jplace(outfile)

> tr2
'treedata' S4 object that stored information
of
        '/tmp/RtmpMNu1tc/file5df3c448e1d'.

...@ phylo:

Phylogenetic tree with 13 tips and 12 internal nodes.

Tip labels:
  A, B, C, D, E, F, ...

Rooted; includes branch lengths.

with the following features available:
  'nplace'.

# The associated data tibble abstraction: 25 × 4
# The 'node', 'label' and 'isTip' are from the phylo tree.
    node label isTip nplace
   <int> <chr> <lgl>  <dbl>
 1     1 A     TRUE       0
 2     2 B     TRUE       0
 3     3 C     TRUE       0
 4     4 D     TRUE       0
 5     5 E     TRUE       0
 6     6 F     TRUE       1
 7     7 G     TRUE       0
 8     8 H     TRUE       0
 9     9 I     TRUE       0
10    10 J     TRUE       0
# ℹ 15 more rows
# ℹ Use `print(n = ...)` to see more rows