tree_subset: Subset tree objects by related nodes

In treeio: Base Classes and Functions for Phylogenetic Tree Input and Output

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

## Not run: 
  nwk <- system.file("extdata", "sample.nwk", package="treeio")
  tree <- read.tree(nwk)

  sub_tree <- tree_subset(tree, node = "A", levels_back = 3)
  ggtree(sub_tree) + geom_tiplab() + geom_nodelab()

## End(Not run)

## Not run: 
  nwk <- system.file("extdata", "sample.nwk", package="treeio")
  tree <- read.tree(nwk)

  sub_tree <- tree_subset(tree, node = "A", levels_back = 3)
  ggtree(sub_tree) + geom_tiplab() + geom_nodelab()

## End(Not run)

treeio documentation built on Nov. 21, 2020, 2:01 a.m.