| ggdensitree {ggtree} | R Documentation |
drawing phylogenetic trees from list of phylo objects
ggdensitree( data = NULL, mapping = NULL, layout = "slanted", tip.order = "mds_dist", align.tips = TRUE, jitter = 0, ... )
data |
a list of phylo objects or any object with an as.phylo and fortify method |
mapping |
aesthetic mapping |
layout |
one of 'slanted', 'rectangluar', 'fan', 'circular' or 'radial' (default: 'slanted') |
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; 'mds' to order the tips based on MDS of the path length between the tips; or 'mds_dist' to order the tips based on MDS of the distance between the tips (default: 'mds_dist') |
align.tips |
TRUE to align trees by their tips and FALSE to align trees by their root (default: TRUE) |
jitter |
deviation to jitter tips |
... |
additional parameters passed to fortify, ggtree and geom_tree |
tree layer
Yu Guangchuang, Bradley R. Jones
require(ape)
require(dplyr)
# Plot mutliple 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 aligmned tips with tip labls 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)
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)))
})
# Plot multiple trees with aligned tips from muliple time points
ggdensitree(time.trees, aes(colour=tree), tip.order=paste0("t", 1:10)) + geom_tiplab(colour='black')
# Read example data
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"))
trees <- lapply(trees, groupOTU, grp)
# Plot multiple trees colored by OTU
ggdensitree(trees, aes(colour=group), alpha=1/6) + scale_colour_manual(values=c("black", "red", "green", "blue"))