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,
  to.root = FALSE
)

Arguments

vector	a vector of variables (equal to the number of tips or to the number of tips and nodes) or a vector of tips and nodes names or IDs.
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).
to.root	logical, if vector is a list of tips and nodes, whether to colour internal edges all the way to the root (TRUE) or not (FALSE - default).

Value

If the input vector is a vector of variables, the function returns 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"). Else it returns an integer vector for the selected edges.

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)

## Matching the tips and nodes colours to the root
data(bird.orders)

## Getting the bird orders starting with a "C"
some_orders <- sort(bird.orders$tip.label)[4:9]

## Get the edges linking these orders
edges_of_interest <- match.tip.edge(vector = some_orders,
                                    phylo  = bird.orders)

## Create a colour vector for all edges
all_edges <- rep("grey", Nedge(bird.orders))
## Replacing the edges of interest by another colour
all_edges[edges_of_interest] <- "black"

## Plot the results
plot(bird.orders, edge.color = all_edges)

TGuillerme/dispRity documentation built on Jan. 26, 2025, 5:37 a.m.