Package 'treeio'

Title: Base Classes and Functions for Phylogenetic Tree Input and Output
Description: 'treeio' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file and can be served as a platform for merging tree with associated data and converting file formats.
Authors: Guangchuang Yu [aut, cre] , Tommy Tsan-Yuk Lam [ctb, ths], Shuangbin Xu [ctb] , Bradley Jones [ctb], Casey Dunn [ctb], Tyler Bradley [ctb], Konstantinos Geles [ctb]
Maintainer: Guangchuang Yu <[email protected]>
License: Artistic-2.0
Version: 1.31.0
Built: 2024-10-30 09:17:31 UTC
Source: https://github.com/YuLab-SMU/treeio

Help Index

as.treedata

Description

convert phylo to treedata

Usage

## S3 method for class 'phylo'
as.treedata(tree, boot = NULL, ...)

Arguments

tree

input tree, a phylo object
boot

optional, can be bootstrap value from ape::boot.phylo
...

additional parameters

Details

converting phylo object to treedata object

Author(s)

Guangchuang Yu

find the hierarchical cluster analysis among the nodes of graph based on the length of all the shortest paths in the graph.

Description

find the hierarchical cluster analysis among the nodes of graph based on the length of all the shortest paths in the graph.

Usage

find.hclust(
  x,
  graph.mst = FALSE,
  weights = NULL,
  hclust.method = "average",
  ...
)

Arguments

x

a igraph object
graph.mst

logical whether obtain the minimum spanning tree first then find.hclust, default is FALSE.
weights

a numeric vector giving edge weights or a character. If this is NULL and the graph has a weight edge attribute, then the attribute is used. If this is NA then no weights are used even if the graph has a weight attribute. If this is a character, the graph has the edge attribute which is numeric, then it will be used, default is NULL.
hclust.method

the agglomeration method to be used, This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).
...

additional parameters

Value

hclust object

Examples

library(igraph)
set.seed(123)
g <- igraph::sample_gnp(100, .1) %>%
     set_edge_attr(name='weight', value=abs(rnorm(E(.),3)))
tr1 <- find.hclust(g, weights = NA)
tr2 <- find.hclust(g)
tr3 <- find.hclust(g, graph.mst = TRUE)

get.placements

Description

access placement information

Usage

get.placements(tree, ...)

## S3 method for class 'jplace'
get.placements(tree, by = "best", ...)

Arguments

tree

tree object
...

additional parameters
by

one of 'best' and 'all'

Value

placement tibble

get.tree

Description

access phylo slot

Usage

get.tree(x, ...)

Arguments

x

tree object
...

additional parameters

Value

phylo object

Author(s)

Guangchuang Yu

get.treetext method

Description

access tree text (newick text) from tree object

Usage

get.treetext(object, ...)

Arguments

object

treedata object
...

additional parameter

Value

phylo object

getNodeNum

Description

calculate total number of nodes

Usage

getNodeNum(tree)

Nnode2(tree)

Arguments

tree

tree object

Value

number

Author(s)

Guangchuang Yu

Examples

getNodeNum(rtree(30))
Nnode2(rtree(30))

is.ggtree

Description

test whether input object is produced by ggtree function

Usage

is.ggtree(x)

Arguments

x

object

Value

TRUE or FALSE

Author(s)

Guangchuang Yu

Class "jplace" This class stores phylogenetic placements

Description

Class "jplace" This class stores phylogenetic placements

Slots

phylo

phylo object for tree structure

treetext

newick tree string

data

associated data

extraInfo

extra information, reserve for merge_tree

file

tree file

placements

reserve for jplace file to store placement information

info

extra information, e.g. metadata, software version etc.

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

label_branch_paml

Description

label branch for PAML to infer selection pressure using branch model

Usage

label_branch_paml(tree, node, label)

Arguments

tree

phylo object
node

node number
label

label of branch, e.g. #1

Value

updated phylo object

Author(s)

Guangchuang Yu

mask

Description

site mask

Usage

mask(tree_object, field, site, mask_site = FALSE)

Arguments

tree_object

tree object
field

selected field
site

site
mask_site

if TRUE, site will be masked. if FALSE, selected site will not be masked, while other sites will be masked.

Value

updated tree object

Author(s)

Guangchuang Yu

merge_tree

Description

merge two tree object

Usage

merge_tree(obj1, obj2)

Arguments

obj1

tree object 1
obj2

tree object 2

Value

tree object

Author(s)

Guangchuang Yu

print

Description

print information of a list of treedata objects

Usage

## S3 method for class 'treedataList'
print(x, ...)

Arguments

x

a list of treedata objects
...

no used

Value

message

raxml2nwk

Description

convert raxml bootstrap tree to newick format

Usage

raxml2nwk(infile, outfile = "raxml.tree")

Arguments

infile

input file
outfile

output file

Value

newick file

Author(s)

Guangchuang Yu

read.astral

Description

parse ASTRAL output newick text

Usage

read.astral(file)

Arguments

file

ASTRAL Newick file

Value

treedata object

Author(s)

Guangchuang Yu

Examples

tt <- paste0(
  "((species1,(species2,species3)'[pp1=0.75;pp2=0.24;pp3=0.01]':",
  "1.2003685744180805)'[pp1=0.98;pp2=0.02;pp3=0]':0.9679599282730038,",
  "((species4,species5)'[pp1=0.88;pp2=0.11;pp3=0.01]':1.2454851536484994))"
)
read.astral(textConnection(tt))

read.beast

Description

read beast/mrbayes/mega Nexus output

read beast/mrbayes/mega newick file format

Usage

read.beast(file, threads = 1, verbose = FALSE)

read.mrbayes(file, threads = 1, verbose = FALSE)

read.beast.newick(file, threads = 1, verbose = FALSE)

read.mega(file, threads = 1, verbose = FALSE)

Arguments

file

newick file
threads

number of threads for multithreading (default: 1)
verbose

set TRUE to log progress (default: FALSE)

Value

treedata object

treedata object

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

Bradley R Jones

Examples

file <- system.file("extdata/BEAST", "beast_mcc.tree", package="treeio")
read.beast(file)
file <- system.file("extdata/MrBayes", "Gq_nxs.tre", package="treeio")
read.mrbayes(file)
tr <- read.beast.newick(
        textConnection(
          '(a[&rate=1]:2,(b[&rate=1.1]:1,c[&rate=0.9]:1)[&rate=1]:1);'
        )
)

read.codeml

Description

read baseml output

Usage

read.codeml(rstfile, mlcfile, tree = "mlc", type = "Joint")

Arguments

rstfile

rst file
mlcfile

mlc file
tree

one of 'mlc' or 'rst'
type

one of 'Marginal' or 'Joint'

Value

A treedata object

Author(s)

Guangchuang Yu

Examples

rstfile <- system.file("extdata/PAML_Codeml", "rst", package="treeio")
mlcfile <- system.file("extdata/PAML_Codeml", "mlc", package="treeio")
read.codeml(rstfile, mlcfile)

read.codeml_mlc

Description

read mlc file of codeml output

Usage

read.codeml_mlc(mlcfile)

Arguments

mlcfile

mlc file

Value

A codeml_mlc object

Author(s)

Guangchuang Yu

Examples

mlcfile <- system.file("extdata/PAML_Codeml", "mlc", package="treeio")
read.codeml_mlc(mlcfile)

read.fasta

Description

read FASTA file

Usage

read.fasta(fasta, type = "auto")

Arguments

fasta

fasta file
type

sequence type of the input file, one of 'NT' or 'AA'. Default is 'auto' and guess the sequence type automatically

Details

This function supports both DNA or AA sequences

Value

DNAbin or AAbin object

Author(s)

Guangchuang Yu

read.hyphy

Description

read HYPHY output

Usage

read.hyphy(nwk, ancseq, tip.fasfile = NULL)

Arguments

nwk

tree file in nwk format, one of hyphy output
ancseq

ancestral sequence file in nexus format, one of hyphy output
tip.fasfile

tip sequence file

Value

A hyphy object

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

Examples

nwk <- system.file("extdata/HYPHY", "labelledtree.tree", package="treeio")
ancseq <- system.file("extdata/HYPHY", "ancseq.nex", package="treeio")
read.hyphy(nwk, ancseq)

read.hyphy.seq

Description

parse sequences from hyphy output

Usage

read.hyphy.seq(file)

Arguments

file

output of hyphy ancestral sequence inference; nexus format

Value

DNAbin object

Author(s)

Guangchuang Yu

Examples

ancseq <- system.file("extdata/HYPHY", "ancseq.nex", package="treeio")
read.hyphy.seq(ancseq)

read.iqtree

Description

parse IQ-TREE output

Usage

read.iqtree(file)

Arguments

file

IQ-TREE Newick text

Value

treedata object

Author(s)

Guangchuang Yu

read.jplace

Description

read jplace file

Usage

read.jplace(file)

Arguments

file

jplace file

Value

jplace instance

Author(s)

Guangchuang Yu

Examples

jp <- system.file("extdata", "sample.jplace", package="treeio")
read.jplace(jp)

read.jtree

Description

Import tree data from jtree file, which is JSON-based text and probably output by write.jtree

Usage

read.jtree(file)

Arguments

file

tree file

Value

treedata object

Author(s)

Guangchuang Yu

read.mcmctree

Description

read MCMCTree output Tree

Usage

read.mcmctree(file, force.ultrametric = FALSE)

Arguments

file

the output tree file of MCMCTree
force.ultrametric

logical whether convert the tree to be ultrametric, if it is not ultrametric, default is FALSE. When the tree is ultrametric, branch times will be calculated automatically.

Value

treedata object

Examples

file <- system.file("extdata/MCMCTree", "mcmctree_output.tree", package="treeio")
tr <- read.mcmctree(file)
tr

read.mega_tabular

Description

parse tabular output of MEGA

Usage

read.mega_tabular(file)

Arguments

file

MEGA tabular file

Value

treedata object

Author(s)

Guangchuang Yu

read.newick

Description

read newick tree

Usage

read.newick(file, node.label = "label", ...)

Arguments

file

newick file
node.label

parse node label as 'label' or 'support' value
...

additional parameter, passed to 'read.tree'

Value

phylo or treedata object

Author(s)

Guangchuang Yu

read.nextstrain.json

Description

read.nextstrain.json

Usage

read.nextstrain.json(x)

Arguments

x

the json tree file of auspice from nextstrain.

Value

treedata object

Author(s)

Shuangbin Xu

Examples

file1 <- system.file("extdata/nextstrain.json", "minimal_v2.json", package="treeio") 
tr <- read.nextstrain.json(file1)
tr

read.nhx

Description

read nhx tree file

Usage

read.nhx(file)

Arguments

file

nhx file

Value

nhx object

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

Examples

nhxfile <- system.file("extdata/NHX", "ADH.nhx", package="treeio")
read.nhx(nhxfile)

read.paml_rst

Description

read rst file from paml (both baseml and codeml) output

Usage

read.paml_rst(rstfile, type = "Joint")

Arguments

rstfile

rst file
type

one of 'Marginal' or 'Joint'

Value

A treedata object

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

Examples

rstfile <- system.file("extdata/PAML_Baseml", "rst", package="treeio")
read.paml_rst(rstfile)

read.phylip

Description

parsing phylip tree format

Usage

read.phylip(file)

Arguments

file

phylip file

Value

an instance of 'phylip'

Author(s)

Guangchuang Yu

Examples

phyfile <- system.file("extdata", "sample.phy", package="treeio")
read.phylip(phyfile)

read.phylip.seq

Description

read aligned sequences from phylip format

Usage

read.phylip.seq(file)

Arguments

file

phylip file, currently only sequential format is supported

Value

DNAbin object

Author(s)

Guangchuang Yu

References

http://evolution.genetics.washington.edu/phylip/doc/sequence.html

read.phylip.tree

Description

parse tree from phylip file

Usage

read.phylip.tree(file)

Arguments

file

phylip file

Value

phylo or multiPhylo object

Author(s)

Guangchuang Yu

read.phyloxml

Description

read.phyloxml

Usage

read.phyloxml(file)

Arguments

file

phyloxml file

Value

treedata class or treedataList class

Examples

xmlfile1 <- system.file("extdata/phyloxml", "test_x2.xml", package="treeio")
px1 <- read.phyloxml(xmlfile1)
px1
xmlfile2 <- system.file("extdata/phyloxml", "phyloxml_examples.xml", package="treeio")
px2 <- read.phyloxml(xmlfile2)
px2

read.r8s

Description

parse output from r8s

Usage

read.r8s(file)

Arguments

file

r8s output log file

Value

multiPhylo object

Author(s)

Guangchuang Yu

Examples

read.r8s(system.file("extdata/r8s", "H3_r8s_output.log", package="treeio"))

read.raxml

Description

parse RAxML bootstrapping analysis output

Usage

read.raxml(file)

Arguments

file

RAxML bootstrapping analysis output

Value

treedata object

Author(s)

Guangchuang Yu

Examples

raxml_file <- system.file("extdata/RAxML", "RAxML_bipartitionsBranchLabels.H3", package="treeio")
read.raxml(raxml_file)

read.treeqza

Description

read.treeqza

Usage

read.treeqza(treeqza, node.label = "label", ...)

Arguments

treeqza

the qiime2 output file contained tree file.
node.label

parse node label as 'label' or 'support' value.
...

additional parameter, passed to 'read.tree'.

Value

phylo tree object or treedata object when node.label was parsed 'support'.

Examples

qzafile1 <- system.file("extdata/qiime2treeqza", "fasttree-tree.qza", package="treeio")
qzafile2 <- system.file("extdata/qiime2treeqza", "iqt-tree.qza", package="treeio")
qzafile3 <- system.file("extdata/qiime2treeqza", "raxml-cat-tree.qza", package="treeio")
tr1 <- read.treeqza(qzafile1)
tr1
tr2 <- read.treeqza(qzafile2)
tr2
tr3 <- read.treeqza(qzafile3)
tr3
# parse node label as 'support' value.
qzafile4 <- system.file("extdata/qiime2treeqza", "raxml-cat-bootstrap-tree.qza", package="treeio")
tr4 <- read.treeqza(qzafile4, node.label="support")
tr4

read.timetree

Description

read timetree output

Usage

read.treetime(file)

read.timetree(file)

Arguments

file

the output tree file of timetree

Value

treedata object

rename_taxa

Description

rename tip label of phylogenetic tree

Usage

rename_taxa(tree, data, key = 1, value = 2)

Arguments

tree

tree object, either treedata or phylo
data

data frame
key

column in data that match tip label (use 1st column by default)
value

column in data for rename tip label (use 2nd column by default)

Value

tree object

Author(s)

Guangchuang Yu

Examples

tree <- rtree(3)
d <- data.frame(old = paste0('t', 1:3), new = LETTERS[1:3])
rename_taxa(tree, d)
rename_taxa(tree, d, old, new)

rescale_tree

Description

rescale branch length of tree object

Usage

rescale_tree(tree_object, branch.length)

Arguments

tree_object

tree object
branch.length

numerical features (e.g. dN/dS)

Value

update tree object

Author(s)

Guangchuang Yu

spt method

Description

spt method

Usage

spt(x, from, to, weights = NULL, ...)

Arguments

x

a igraph object
from

a specific node of network.
to

other nodes of the network, length of it must be larger than 2.
weights

a numeric vector giving edge weights or a character. If this is NULL and the graph has a weight edge attribute, then the attribute is used. If this is NA then no weights are used even if the graph has a weight attribute. If this is a character, the graph has the edge attribute which is numeric, then it will be used, default is NULL.
...

additional parameters

Value

phylo object

Examples

library(igraph)
set.seed(123)
g <- igraph::sample_gnp(100, .1) %>% 
     set_edge_attr(name='weight', value=abs(rnorm(E(.),3)))
tr1 <- spt(g, from = 6, to=V(g), weights = 'weight')
tr1
tr2 <- spt(g, from = 6, to = V(g), weights = NA)
tr2

write.beast

Description

Export treedata object to BEAST NEXUS file. This function was adopted and modified from ape::write.nexus

Usage

write.beast(treedata, file = "", translate = TRUE, tree.name = NULL)

Arguments

treedata

treedata object, list of treedata, phylo, or list of phylo
file

output file. If file = "", print the output content on screen
translate

whether to translate taxa labels
tree.name

names of the trees, NULL to use existing tree names

Value

output file or file content on screen

Author(s)

Guangchuang Yu

Examples

nhxfile <- system.file("extdata/NHX", "phyldog.nhx", package="treeio")
nhx <- read.nhx(nhxfile)
write.beast(nhx)

write.beast.newick

Description

Export treedata object to BEAST Newick file. This is useful for making BEAST starting trees with metadata

Usage

write.beast.newick(
  treedata,
  file = "",
  append = FALSE,
  digits = 10,
  tree.prefix = ""
)

Arguments

treedata

treedata object
file

output file. If file = "", print the output content on screen
append

logical. Only used if the argument 'file' is the name of file (and not a connection or "|cmd"). If 'TRUE' output will be appended to 'file'; otherwise, it will overwrite the contents of file.
digits

integer, the indicating the number of decimal places, default is 10.
tree.prefix

character the tree prefix, default is "".

Value

output file or file content on screen

Author(s)

Guangchuang Yu

Examples

nhxfile <- system.file("extdata/NHX", "phyldog.nhx", package="treeio")
nhx <- read.nhx(nhxfile)
write.beast.newick(nhx)

write.jplace

Description

Export jplace object to jplace file.

Usage

write.jplace(x, outfile)

Arguments

x

a jplace object.
outfile

the output file name

Examples

jp <- system.file("extdata", "sample.jplace", package="treeio")
tr1 <- read.jplace(jp)
outfile <- tempfile()
write.jplace(tr1, outfile)
tr2 <- read.jplace(outfile)
tr2

write.jtree

Description

Export treedata object to json tree file

Usage

write.jtree(treedata, file = "")

Arguments

treedata

treedata object
file

output file. If file = "", print the output content on screen

Value

output file or file content on screen

Author(s)

Guangchuang Yu