makeCollapsedTree: Collapse a tree into a single tip per category

In treespace: Statistical Exploration of Landscapes of Phylogenetic Trees

Collapse a tree into a single tip per category

Description

Reduce a tree with many tips into a tree with a single tip per category. Where a category's tips form a monophyletic clade, the clade is replaced by a single tip labelled by that category. Where a category's tips are paraphyletic, the largest clade for that category is treated as above, and all other tips pruned.

Usage

makeCollapsedTree(tree, df, warnings = TRUE)

Arguments

tree	an object of the class phylo: the tree to collapse.
df	a two-column data frame linking tip labels (column 2) with their corresponding categories (column 1).
warnings	a logical determining whether a warning should be given if there are paraphyletic categories (default TRUE)

Value

A tree (class phylo) whose tip labels are exactly the set of unique categories from df.

Author(s)

Michelle Kendall [e-mail]

See Also

treeConcordance simulateIndTree

Examples

 
# simulate a tree which is monophyletic per category
tree <- simulateIndTree(rtree(5), permuteTips=FALSE)

df <- cbind(sort(rep(rtree(5)$tip.label,5)),sort(tree$tip.label))
palette <- c("red","blue","black","green","purple")#' 
tipCols <- palette[as.factor(sapply(tree$tip.label, function(l) df[which(df[,2]==l),1]))]
plot(tree, tip.color=tipCols)
collapsedTree <- makeCollapsedTree(tree,df)
plot(collapsedTree, tip.color=palette[as.factor(collapsedTree$tip.label)])

# simulate a tree which is paraphyletic per category
tree <- simulateIndTree(rtree(5), tipPercent=20)
tipCols <- palette[as.factor(sapply(tree$tip.label, function(l) df[which(df[,2]==l),1]))]
plot(tree, tip.color=tipCols)
collapsedTree <- makeCollapsedTree(tree,df)
plot(collapsedTree, tip.color=palette[as.factor(collapsedTree$tip.label)])

treespace documentation built on Sept. 8, 2023, 6:04 p.m.