tree_subset {treeio} | R Documentation

## 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)

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

    ## S3 method for class 'treedata'
    tree_subset(tree, node, levels_back = 5,
      group_node = 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

### 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)

[Package treeio version 1.6.2 Index]