ggdensitree(
  data = NULL,
  mapping = NULL,
  layout = "slanted",
  tip.order = "mode",
  align.tips = TRUE,
  jitter = 0,
  ...
)

require(ape)
require(dplyr)
require(tidyr)

# Plot multiple trees with aligned tips
trees <- list(read.tree(text="((a:1,b:1):1.5,c:2.5);"), read.tree(text="((a:1,c:1):1,b:2);"));
ggdensitree(trees) + geom_tiplab()

# Plot multiple trees with aligned tips with tip labels and separate tree colors
trees.fort <- list(trees[[1]] %>% fortify %>% mutate(tree="a"), trees[[2]] %>% fortify %>% mutate(tree="b"));
ggdensitree(trees.fort, aes(colour=tree)) + geom_tiplab(colour='black')


# Generate example data
set.seed(1)
random.trees <- rmtree(5, 10)
time.trees <- lapply(seq_along(random.trees), function(i) {
 	tree <- random.trees[[i]]
 	tree$tip.label <- paste0("t", 1:10)
	dates <- estimate.dates(tree, 1:10, mu=1, nsteps=1)
	tree$edge.length <- dates[tree$edge[, 2]] - dates[tree$edge[, 1]]
	fortify(tree) %>% mutate(tree=factor(i, levels=as.character(1:10)))
})

# Plot multiple trees with aligned tips from multiple time points
ggdensitree(time.trees, aes(colour=tree), tip.order=paste0("t", 1:10)) + geom_tiplab(colour='black')


# Read example data
example.trees <- read.tree(system.file("examples", "ggdensitree_example.tree", package="ggtree"))

# Compute OTU
grp <- list(A = c("a.t1", "a.t2", "a.t3", "a.t4"), B = c("b.t1", "b.t2", "b.t3", "b.t4"), C = c("c.t1", "c.t2", "c.t3", "c.t4"))
otu.trees <- lapply(example.trees, groupOTU, grp)

# Plot multiple trees colored by OTU
ggdensitree(otu.trees, aes(colour=group), alpha=1/6, tip.order='mds') + scale_colour_manual(values=c("black", "red", "green", "blue"))