dispRity (version 1.7.0)

slide.nodes: Stretching a tree

Description

Stretches a phylogenetic tree at a particular node

Usage

slide.nodes(nodes, tree, slide)

Value

A "phylo" object.

Arguments

nodes

A list of the ID nodes to slide ("integer"). The first node is ape::Ntip(tree) + 1, etc.

tree

a "phylo" object.

slide

the sliding value.

Author

Thomas Guillerme

Details

The sliding works by subtracting the slide value to the branch leading to the node and adding it to the descendant branches. Note that the slide value can be negative to slide nodes the other way (up); the only requirement is that the slide does not lead to negative branch length values.

See Also

remove.zero.brlen

Examples

set.seed(42)
## Generating a coalescent tree
tree <- rcoal(5)

## Stretching node 8 up and down
tree_slide_up <- slide.nodes(8, tree, slide = 0.075)
tree_slide_down <- slide.nodes(8, tree, slide = -0.075)

## Display the results
par(mfrow = c(3,1))
plot(tree) ; axisPhylo() ; nodelabels()
plot(tree_slide_up) ; axisPhylo() ; nodelabels()
plot(tree_slide_down) ; axisPhylo() ; nodelabels()

## Stretching many nodes
set.seed(42)
tree <- rtree(50)
move_nodes <- c(99, 93, 53, 86, 58, 63, 60, 84)
tree_slided <- slide.nodes(move_nodes, tree, slide = 0.07)

## Display the results
par(mfrow = c(2, 1))
node_colors <- c("lightblue", "orange")[((1:Nnode(tree))+Ntip(tree)) %in% move_nodes + 1]
plot(tree, show.tip.label = FALSE) ; axisPhylo()
nodelabels(bg = node_colors, cex = 0.5)
plot(tree_slided, show.tip.label = FALSE) ; axisPhylo()
nodelabels(bg = node_colors, cex = 0.5)