Package 'tidytree'

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

See Also

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_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

---

get.data method

Description

get.data method

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))

---

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

---

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))

---

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)

---

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

---