subtreeShow function

Highlight a subtree

Highlight a subtree

Plot a tree, highlighting the clade(s) descending from the given node(s)

subtreeShow( tree, nodeList, showNodeLabels = "nodeList", mainCol = "black", subtreeCol = "red", nodeLabelCol = "lightblue", ... )

Arguments

  • tree: a tree of class phylo or phylo4. The tree should be binary and rooted; if not it will be coerced into a binary rooted tree using multi2di, if possible.
  • nodeList: a list of one or more internal nodes in the tree.
  • showNodeLabels: option of whether to show node labels. Default is "nodeList", which only labels the nodes in nodeList. Choosing showNodeLabels="all" will display all node labels; any other arguments will remove all node labels.
  • mainCol: colour for the edges which are not highlighted (default is black).
  • subtreeCol: colour for the edges which are highlighted (default is red).
  • nodeLabelCol: background colour for any node labels shown (default is light blue)
  • ...: further arguments to be passed to plot.phylo

Returns

A plot of the tree, with clade(s) descending from the given node(s) highlighted.

Examples

## Highlight the clade(s) descending from nodes 23 and 35 in a random tree on 20 tips: tree <- rtree(20) subtreeShow(tree, nodeList=c(23,35)) # change aesthetics: subtreeShow(tree,nodeList=c(23,35), mainCol="navy", subtreeCol="cyan", nodeLabelCol="cyan", edge.width=2)

Author(s)

Michelle Kendall michelle.louise.kendall@gmail.com

  • Maintainer: Michelle Kendall
  • License: GPL-2
  • Last published: 2023-01-24