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
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() }