Help for package tidytree

Title:

A Tidy Tool for Phylogenetic Tree Data Manipulation

Version:

0.4.6

Description:

Phylogenetic tree generally contains multiple components including node, edge, branch and associated data. 'tidytree' provides an approach to convert tree object to tidy data frame as well as provides tidy interfaces to manipulate tree data.

Depends:

R (≥ 3.4.0)

Imports:

ape, dplyr, lazyeval, magrittr, methods, rlang, tibble, tidyr, tidyselect, yulab.utils (≥ 0.0.4), pillar, cli

Suggests:

knitr, rmarkdown, prettydoc, testthat, utils

VignetteBuilder:

knitr

ByteCompile:

true

License:

Artistic-2.0

URL:

https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/

BugReports:

https://github.com/YuLab-SMU/tidytree/issues

Encoding:

UTF-8

RoxygenNote:

7.2.3

NeedsCompilation:

Packaged:

2023-12-12 11:11:12 UTC; HUAWEI

Author:

Guangchuang Yu

[aut, cre, cph], Bradley Jones [ctb], Zebulun Arendsee [ctb]

Maintainer:

Guangchuang Yu <guangchuangyu@gmail.com>

Repository:

CRAN

Date/Publication:

2023-12-12 11:40:02 UTC

MRCA

Description

access most recent common ancestor data

Usage

MRCA(.data, ...)

Arguments

.data

phylo or tbl_tree object

...

additional parameters

Value

MRCA data

Author(s)

Guangchuang Yu

Nnode

Description

number of nodes

Usage

## S3 method for class 'treedata'
Nnode(phy, internal.only = TRUE, ...)

Arguments

phy

treedata object

internal.only

whether only count internal nodes

...

additional parameters

Value

number of nodes

Author(s)

Guangchuang Yu

Examples

Nnode(rtree(30))

ancestor

Description

access ancestor data

Usage

ancestor(.data, .node, ...)

## S3 method for class 'tbl_tree'
ancestor(.data, .node, ...)

Arguments

.data

phylo or tbl_tree object

.node

node number

...

additional parameters

Value

ancestor data

Author(s)

Guangchuang Yu

Examples

library(ape)
tree <- rtree(4)
x <- as_tibble(tree)
ancestor(x, 3)

as.treedata

Description

convert a tree object to treedata object

Usage

as.treedata(tree, ...)

## S3 method for class 'tbl_tree'
as.treedata(tree, ...)

Arguments

tree

tree object

...

additional parameters

Value

treedata object

Examples

library(ape)
set.seed(2017)
tree <- rtree(4)
d <- tibble(label = paste0('t', 1:4),
           trait = rnorm(4))
x <- as_tibble(tree)
full_join(x, d, by = 'label') %>% as.treedata

as.ultrametric

Description

as.ultrametric

Usage

as.ultrametric(tree, ...)

Arguments

tree

tree object

...

additional parameters

Value

treedata or phylo object

child

Description

access child data

Usage

child(.data, .node, ...)

## S3 method for class 'tbl_tree'
child(.data, .node, ...)

Arguments

.data

phylo or tbl_tree object

.node

node number

...

additional parameters

Value

child data

Author(s)

Guangchuang Yu

Examples

library(ape)
tree <- rtree(4)
x <- as_tibble(tree)
child(x, 4)

drop.tip method

Description

drop.tip method

Usage

drop.tip(object, tip, ...)

keep.tip(object, tip, ...)

## S4 method for signature 'treedata'
drop.tip(object, tip, ...)

## S4 method for signature 'phylo'
drop.tip(object, tip, ...)

## S4 method for signature 'treedata'
keep.tip(object, tip, ...)

## S4 method for signature 'phylo'
keep.tip(object, tip, ...)

Arguments

object

A treedata or phylo object

tip

a vector of mode numeric or character specifying the tips to delete

...

additional parameters

Value

updated object

Author(s)

Casey Dunn http://dunnlab.org and Guangchuang Yu https://guangchuangyu.github.io

Source

drop.tip for phylo object is a wrapper method of ape::drop.tip from the ape package. The documentation you should read for the drop.tip function can be found here: drop.tip

Examples

library(tidytree)
set.seed(123)
tr <- ape::rtree(6)
da <- data.frame(id=tip.label(tr), value = letters[seq_len(6)])
trda <- tr %>% dplyr::left_join(da, by = c('label'='id'))
tr1 <- drop.tip(tr, c("t2", "t1"))
tr2 <- keep.tip(tr, c("t2", "t1"))

get.data method

Description

get.data method

Usage

get.data(object, ...)

## S4 method for signature 'treedata'
get.data(object)

Arguments

object

treedata object

...

additional parameter

Value

associated data of phylogeny

get.fields method

Description

get.fields method

Usage

get.fields(object, ...)

## S4 method for signature 'treedata'
get.fields(object)

Arguments

object

treedata object

...

additional parameter

Value

available annotation variables

get.treetext method

Description

access tree text (newick text) from tree object

Usage

get.treetext(object, ...)

## S4 method for signature 'treedata'
get.treetext(object)

Arguments

object

treedata object

...

additional parameter

Value

phylo object

getNodeNum

Description

calculate total number of nodes

Usage

getNodeNum(tree)

Arguments

tree

tree object

Value

number

Author(s)

Guangchuang Yu

Examples

getNodeNum(rtree(30))

get_tree_data

Description

get associated data stored in treedata object

Usage

get_tree_data(tree_object)

Arguments

tree_object

a treedata object

Value

tbl_df

Author(s)

guangchuang yu

groupClade

Description

grouping clades

Usage

groupClade(.data, .node, group_name = "group", overlap = "overwrite", ...)

Arguments

.data

tree object (phylo, treedata, tbl_tree, ggtree etc.)

.node

selected nodes

group_name

character the name of the group cluster, default is group.

overlap

character one of overwrite,origin and abandon, default is overwrite.

...

additional parameter

Value

updated tree with group information or group index

Author(s)

Guangchuang Yu

groupOTU

Description

grouping OTUs

Usage

groupOTU(.data, .node, group_name = "group", ...)

Arguments

.data

tree object (phylo, treedata, tbl_tree, ggtree etc.)

.node

selected nodes

group_name

character the name of the group cluster, default is group.

...

additional parameter

Value

updated tree with group information or group index

Author(s)

Guangchuang Yu

isTip

Description

whether the node is a tip

Usage

isTip(.data, .node, ...)

## S3 method for class 'tbl_tree'
isTip(.data, .node, ...)

## S3 method for class 'phylo'
isTip(.data, .node, ...)

## S3 method for class 'treedata'
isTip(.data, .node, ...)

Arguments

.data

phylo, treedata or tbl_tree object

.node

node number

...

additional parameters

Value

logical value

Author(s)

Guangchuang Yu

extract the node label of phylo, treedata or tbl_tree

Description

extract the node label of phylo, treedata or tbl_tree

Usage

node.label(x, node = "internal", ...)

Arguments

x

object, should be one of treedata,phylo or tbl_tree.

node

character, to extract which type node label, default is internal, should be one of internal, external, all, tip.

...

additional parameters.

Value

label character vector.

nodeid

Description

convert tree label to internal node number

Usage

nodeid(tree, label)

Arguments

tree

tree object

label

tip/node label(s)

Value

node number

Author(s)

Guangchuang Yu

nodelab

Description

convert internal node number tip/node label

Usage

nodelab(tree, id)

Arguments

tree

tree object

id

node number

Value

tip/node label(s)

Author(s)

Guangchuang Yu

offspring

Description

access offspring data

Usage

offspring(.data, .node, tiponly, self_include, ...)

## S3 method for class 'tbl_tree'
offspring(.data, .node, tiponly = FALSE, self_include = FALSE, ...)

Arguments

.data

phylo or tbl_tree object

.node

node number

tiponly

whether only return tip nodes

self_include

whether include the input node, only applicable for tiponly = FALSE

...

additional parameters

Value

offspring data

Author(s)

Guangchuang Yu

Examples

library(ape)
tree <- rtree(4)
x <- as_tibble(tree)
offspring(x, 4)

parent

Description

access parent data

Usage

parent(.data, .node, ...)

## S3 method for class 'tbl_tree'
parent(.data, .node, ...)

Arguments

.data

phylo or tbl_tree object

.node

node number

...

additional parameters

Value

parent data

Author(s)

Guangchuang Yu

Examples

library(ape)
tree <- rtree(4)
x <- as_tibble(tree)
parent(x, 2)

Objects exported from other packages

Description

These objects are imported from other packages. Follow the links below to see their documentation.

ape: as.phylo, as.phylo, is.rooted, Nnode, Ntip, read.tree, root, rtree
dplyr: arrange, filter, full_join, left_join, mutate, pull, rename, rename, select, summarise, summarize, transmute
magrittr: %<>%, %>%
rlang: .data
tibble: as_tibble, tibble
tidyr: unnest

root

Description

re-root a tree

Usage

## S3 method for class 'treedata'
root(phy, outgroup, node = NULL, edgelabel = TRUE, ...)

Arguments

phy

tree object

outgroup

a vector of mode numeric or character specifying the new outgroup

node

node to reroot

edgelabel

a logical value specifying whether to treat node labels as edge labels and thus eventually switching them so that they are associated with the correct edges.

...

additional parameters passed to ape::root.phylo

Value

rerooted treedata

rootnode

Description

access root node data

Usage

rootnode(.data, ...)

Arguments

.data

phylo or tbl_tree object

...

additional parameters

Value

root node data

Author(s)

Guangchuang Yu

show method

Description

show method for treedata instance

Usage

show(object)

Arguments

object

treedata object

Value

print info

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

sibling

Description

access sibling data

Usage

sibling(.data, ...)

Arguments

.data

phylo or tbl_tree object

...

additional parameters

Value

sibling

Author(s)

Guangchuang Yu

the tip or internal node label assign of tbl_tree phylo and treedata

Description

the tip or internal node label assign of tbl_tree phylo and treedata

Usage

tip.label(x) <- value

node.label(x) <- value

## S3 replacement method for class 'phylo'
node.label(x) <- value

## S3 replacement method for class 'treedata'
node.label(x) <- value

## S3 replacement method for class 'tbl_tree'
node.label(x) <- value

## S3 replacement method for class 'phylo'
tip.label(x) <- value

## S3 replacement method for class 'treedata'
tip.label(x) <- value

## S3 replacement method for class 'tbl_tree'
tip.label(x) <- value

Arguments

x

object, should be one of tbl_tree, phylo or treedata

value

character, the character vector

extract the tip label of phylo treedata or tbl_tree

Description

extract the tip label of phylo treedata or tbl_tree

Usage

tip.label(x, ...)

Arguments

x

object, should be one of treedata,phylo or tbl_tree.

...

additional parameters.

Subset tree objects by related nodes

Description

This function allows for a tree object to be subset by specifying a node and returns all related nodes within a selected number of levels

Usage

tree_subset(
  tree,
  node,
  levels_back = 5,
  group_node = TRUE,
  group_name = "group",
  root_edge = TRUE
)

## S3 method for class 'phylo'
tree_subset(
  tree,
  node,
  levels_back = 5,
  group_node = TRUE,
  group_name = "group",
  root_edge = TRUE
)

## S3 method for class 'treedata'
tree_subset(
  tree,
  node,
  levels_back = 5,
  group_node = TRUE,
  group_name = "group",
  root_edge = TRUE
)

Arguments

tree

a tree object of class phylo

node

either a tip label or a node number for the given tree that will be the focus of the subsetted tree

levels_back

a number specifying how many nodes back from the selected node the subsetted tree should include

group_node

whether add grouping information of selected node

group_name

group name (default 'group') for storing grouping information if group_node = TRUE

root_edge

If TRUE (by default), set root.edge to path length of orginal root to the root of subset tree

Details

This function will take a tree and a specified node from that tree and subset the tree showing all relatives back to a specified number of nodes. This function allows for a combination of ancestor and offspring to return a subsetted tree that is of class phylo. This allows for easy graphing of the tree with ggtree

Examples

set.seed(123)
tree <- ape::rtree(6)
sub_tree <- tree_subset(tree, node = "t1", levels_back = 2)

treedata

Description

treedata object contructor

Usage

treedata(...)

Arguments

...

parameters

Value

treedata object

Author(s)

guangchuang yu

Class "treedata" This class stores phylogenetic tree with associated data

Description

Class "treedata" This class stores phylogenetic tree with associated data

Slots

file: tree file
treetext: newick tree string
phylo: phylo object for tree structure
data: associated data
extraInfo: extra information, reserve for merge_tree
tip_seq: tip sequences
anc_seq: ancestral sequences
seq_type: sequence type, one of NT or AA
tipseq_file: tip sequence file
ancseq_file: ancestral sequence file
info: extra information, e.g. metadata, software version etc.

Author(s)

Guangchuang Yu https://guangchuangyu.github.io

MRCA

Description

Usage

Arguments

Value

Author(s)

Nnode

Description

Usage

Arguments

Value

Author(s)

Examples

ancestor

Description

Usage

Arguments

Value

Author(s)

Examples

as.treedata

Description

Usage

Arguments

Value

Examples

as.ultrametric

Description

Usage

Arguments

Value

child

Description

Usage

Arguments

Value

Author(s)

Examples

drop.tip method

Description

Usage

Arguments

Value

Author(s)

Source

See Also

Examples

get.data method

Description

Usage

Arguments

Value

get.fields method

Description

Usage

Arguments

Value

get.treetext method

Description

Usage

Arguments

Value

getNodeNum

Description

Usage

Arguments

Value

Author(s)

Examples

get_tree_data

Description

Usage

Arguments

Value

Author(s)

groupClade

Description

Usage

Arguments

Value