read_tree {rbiom} | R Documentation |
Read a newick formatted phylogenetic tree.
Description
A phylogenetic tree is required for computing UniFrac distance matrices. You can load a tree from a file or by providing the tree string directly. This tree must be in Newick format, also known as parenthetic format and New Hampshire format.
Usage
read_tree(src, underscores = FALSE)
Arguments
src |
Input data as either a file path, URL, or Newick string. Compressed (gzip or bzip2) files are also supported. |
underscores |
When parsing the tree, should underscores be kept as
is? By default they will be converted to spaces (unless the entire ID
is quoted). Default |
Value
A phylo
class object representing the tree.
See Also
Other phylogeny:
tree_subset()
Examples
library(rbiom)
infile <- system.file("extdata", "newick.tre", package = "rbiom")
tree <- read_tree(infile)
print(tree)
tree <- read_tree("
(A:0.99,((B:0.87,C:0.89):0.51,(((D:0.16,(E:0.83,F:0.96)
:0.94):0.69,(G:0.92,(H:0.62,I:0.85):0.54):0.23):0.74,J:0.1
2):0.43):0.67);")
plot(tree)
[Package rbiom version 2.2.1 Index]