read nhx tree file
Author
Guangchuang Yu https://guangchuangyu.github.io
Examples
nhxfile <- system.file("extdata/NHX", "ADH.nhx", package="treeio")
read.nhx(nhxfile)
#> 'treedata' S4 object that stored information
#> of
#> '/usr/lib/R/site-library/treeio/extdata/NHX/ADH.nhx'.
#>
#> [email protected] phylo:
#>
#> Phylogenetic tree with 8 tips and 4 internal nodes.
#>
#> Tip labels:
#> ADH2, ADH1, ADHY, ADHX, ADH4, ADH3, ...
#>
#> Rooted; includes branch lengths.
#>
#> with the following features available:
#> 'B', 'D', 'S'.
#>
#> # The associated data tibble abstraction: 12 × 6
#> # The 'node', 'label' and 'isTip' are from the phylo tree.
#> node label isTip B D S
#> <int> <chr> <lgl> <dbl> <chr> <chr>
#> 1 1 ADH2 TRUE NA NA human
#> 2 2 ADH1 TRUE NA NA human
#> 3 3 ADHY TRUE NA NA nematode
#> 4 4 ADHX TRUE NA NA insect
#> 5 5 ADH4 TRUE NA NA yeast
#> 6 6 ADH3 TRUE NA NA yeast
#> 7 7 ADH2 TRUE NA NA yeast
#> 8 8 ADH1 TRUE NA NA yeast
#> 9 9 NA FALSE NA N NA
#> 10 10 NA FALSE NA N metazoa
#> # … with 2 more rows