read_tree: Read a newick formatted phylogenetic tree.

In rbiom: Read/Write, Analyze, and Visualize 'BIOM' Data

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 FALSE

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)

rbiom documentation built on April 3, 2025, 6:39 p.m.