match.tip.edge: Match tips or nodes edge vector

In TGuillerme/dispRity: Measuring Disparity

Match tips or nodes edge vector

Description

Match a vector of tips or tips and nodes with the an edge list from a "phylo" or "multiPhylo".

Usage

match.tip.edge(vector, phylo, replace.na, use.parsimony = TRUE)

Arguments

vector	a vector of variables (equal to the number of tips or to the number of tips and nodes).
phylo	a phylo or multiPhylo object.
replace.na	optional, what to replace NAs with.
use.parsimony	logical, whether to also colour internal edges parsimoniously (TRUE - default; i.e. if two nodes have the same unique ancestor node and the same variable, the ancestor node is assume to be the of the same value as its descendants) or not (FALSE).

Value

A vector of variables equal to the number of edges in the tree (or a list of vectors if the phylo input is of class "multiPhylo").

Author(s)

Thomas Guillerme

Examples

## A random tree
tree <- rtree(20)

## A random vector of two variables for each tips
tip_values <- sample(c("blue", "red"), 20, replace = TRUE)

## Matching the colors (blue and red) to the tips descendants
edge_colors <- match.tip.edge(tip_values, tree, replace.na = "grey")

## Plotting the results
plot(tree, show.tip.label = FALSE, edge.color = edge_colors)
tiplabels(1:20, bg = tip_values)

## Same but without assuming parsimony for the internal nodes
plot(tree, show.tip.label = FALSE,
     edge.color = match.tip.edge(tip_values, tree,
                                 use.parsimony = FALSE,
                                 replace.na = "grey"))

## Matching the tips and nodes colors with the edges
node_values <- sample(c("blue", "red"), 19, replace = TRUE)
edge_colors <- match.tip.edge(c(tip_values, node_values), tree)
plot(tree, show.tip.label = FALSE, edge.color = edge_colors) 
tiplabels(1:20, bg = tip_values)
nodelabels(1:19, bg = node_values)

TGuillerme/dispRity documentation built on April 17, 2024, 10 p.m.