read nhx tree file
read.nhx(file)
Arguments
| file | nhx file |
|---|
Value
nhx object
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/local/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 #> 11 11 NA FALSE 100 Y primates #> 12 12 NA FALSE NA NA Fungi