tree_subset: Subset tree objects by related nodes

In YuLab-SMU/tidytree: A Tidy Tool for Phylogenetic Tree Data Manipulation

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)

YuLab-SMU/tidytree documentation built on July 30, 2024, 8:07 p.m.