ggdensitree: ggdensitree

In YuLab-SMU/ggtree: an R package for visualization of tree and annotation data

ggdensitree

Description

drawing phylogenetic trees from list of phylo objects

Usage

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

Arguments

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; 'mode' to order the tips by the most common order; '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: 'mode')
align.tips	TRUE (default) to align trees by their tips and FALSE to align trees by their root
jitter	deviation to jitter tips
...	additional parameters passed to fortify, ggtree and geom_tree

Details

The trees plotted by 'ggdensitree()' will be stacked on top of each other and the structures of the trees will be rotated to ensure the consistency of the tip order.

Value

tree layer

Author(s)

Yu Guangchuang, Bradley R. Jones

References

For more detailed demonstration of this function, please refer to chapter 4.4.2 of Data Integration, Manipulation and Visualization of Phylogenetic Trees http://yulab-smu.top/treedata-book/index.html by Guangchuang Yu.

Examples

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"))

YuLab-SMU/ggtree documentation built on Nov. 3, 2024, 4:15 p.m.