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 phylo
tree_subset(
tree,
node,
levels_back = 5,
group_node = TRUE,
group_name = "group",
root_edge = TRUE
)
# S3 method for 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
if (FALSE) {
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()
}
if (FALSE) {
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()
}