ggdensitree: ggdensitree

In ggtree: an R package for visualization of tree and annotation data

Description

drawing phylogenetic trees from list of phylo objects

Usage

ggdensitree(
  data = NULL,
  mapping = NULL,
  layout = "slanted",
  tip.order = "mds_dist",
  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; '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

Value

tree layer

Author(s)

Yu Guangchuang, Bradley R. Jones

Examples

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"))

Example output

Registered S3 method overwritten by 'treeio':
  method     from
  root.phylo ape 
ggtree v2.4.1  For help: https://yulab-smu.top/treedata-book/

If you use ggtree in published research, please cite the most appropriate paper(s):

[36m-[39m Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi:10.1002/cpbi.96
[36m-[39m Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194
[36m-[39m Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36. doi:10.1111/2041-210X.12628


Loading required package: ape

Attaching package: ‘ape’

The following object is masked from ‘package:ggtree’:

    rotate

Loading required package: dplyr

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Warning message:
`mutate_()` is deprecated as of dplyr 0.7.0.
Please use `mutate()` instead.
See vignette('programming') for more help
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated. 

ggtree documentation built on Nov. 15, 2020, 2:09 a.m.