rbiom (version 2.2.1)

read_tree: 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)

Value

A phylo class object representing the tree.

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 FALSE

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)