% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ggdensitree.R
ggdensitree(data = NULL, mapping = NULL, layout = "slanted",
  tip.order = "mds", align.tips = TRUE, jitter = 0, ...)
\item{data}{a list of phylo objects or any object with an as.phylo and fortify method}

\item{mapping}{aesthetic mapping}

\item{layout}{one of 'slanted', 'rectangluar', 'fan', 'circular' or 'radial' (default: 'slanted')}

\item{tip.order}{the order of the tips by a character vector of taxa names; or an integer, N, to order the tips by the order of the tips in the Nth tree; or 'mds' to order the tips based on MDS of the distance between the tips (default: 'mds')}

\item{align.tips}{TRUE to align trees by their tips and FALSE to align trees by their root (default: TRUE)}

\item{jitter}{deviation to jitter tips}

\item{...}{additional parameters passed to fortify, ggtree and geom_tree}
tree layer
drawing phylogenetic trees from list of phylo objects

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()

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')

trees <- rmtree(5, 10)
time.trees <- lapply(1:length(trees), function(i) {
 	tree <- 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)))
ggdensitree(time.trees, aes(colour=tree), tip.order=paste0("t", 1:10)) + geom_tiplab(colour='black')
Yu Guangchuang, Bradley R. Jones