Visualize tree with associated matrix

The gheatmap function is designed to visualize phylogenetic tree with heatmap of associated matrix.

In the following example, we visualized a tree of H3 influenza viruses with their associated genotype.

beast_file <- system.file("examples/MCC_FluA_H3.tree", package="ggtree")
beast_tree <- read.beast(beast_file)

genotype_file <- system.file("examples/Genotype.txt", package="ggtree")
genotype <- read.table(genotype_file, sep="\t", stringsAsFactor=F)
colnames(genotype) <- sub("\\.$", "", colnames(genotype))
p <- ggtree(beast_tree, mrsd="2013-01-01") + geom_treescale(x=2008, y=1, offset=2)
p <- p + geom_tiplab(size=2)
gheatmap(p, genotype, offset = 5, width=0.5, font.size=3, colnames_angle=-45, hjust=0) +
    scale_fill_manual(breaks=c("HuH3N2", "pdm", "trig"), values=c("steelblue", "firebrick", "darkgreen"))

The width parameter is to control the width of the heatmap. It supports another parameter offset for controlling the distance between the tree and the heatmap, for instance to allocate space for tip labels.

For time-scaled tree, as in this example, it’s more often to use x axis by using theme_tree2. But with this solution, the heatmap is just another layer and will change the x axis. To overcome this issue, we implemented scale_x_ggtree to set the x axis more reasonable.

p <- ggtree(beast_tree, mrsd="2013-01-01") + geom_tiplab(size=2, align=TRUE, linesize=.5) + theme_tree2()
pp <- (p + scale_y_continuous(expand=c(0, 0.3))) %>%
    gheatmap(genotype, offset=8, width=0.6, colnames=FALSE) %>%
        scale_x_ggtree()
pp + theme(legend.position="right")

Visualize tree with multiple sequence alignment

With msaplot function, user can visualize multiple sequence alignment with phylogenetic tree, as demonstrated below:

fasta <- system.file("examples/FluA_H3_AA.fas", package="ggtree")
msaplot(ggtree(beast_tree), fasta)

A specific slice of the alignment can also be displayed by specific window parameter.

msaplot(ggtree(beast_tree), fasta, window=c(150, 200)) + coord_polar(theta='y')

Annotate a phylogenetic tree with insets

ggtree provides a function, inset, for adding subplots to a phylogenetic tree. The input is a tree graphic object and a named list of ggplot graphic objects (can be any kind of charts), these objects should named by node numbers. To facilitate adding bar and pie charts (e.g. summarized stats of results from ancestral reconstruction) to phylogenetic tree, ggtree provides nodepie and nodebar functions to create a list of pie or bar charts.

set.seed(2015-12-31)
tr <- rtree(15)
p <- ggtree(tr)

a <- runif(14, 0, 0.33)
b <- runif(14, 0, 0.33)
c <- runif(14, 0, 0.33)
d <- 1 - a - b - c
dat <- data.frame(a=a, b=b, c=c, d=d)
## input data should have a column of `node` that store the node number
dat$node <- 15+1:14

## cols parameter indicate which columns store stats (a, b, c and d in this example)
bars <- nodebar(dat, cols=1:4)

inset(p, bars)

inset(p, bars, width=.06, height=.1)

bars2 <- nodebar(dat, cols=1:4, position='dodge',
                 color=c(a='blue', b='red', c='green', d='cyan'))
p2 <- inset(p, bars2, x='branch', width=.06, vjust=-.3)
print(p2)

pies <- nodepie(dat, cols=1:4, alpha=.6)
inset(p, pies)

inset(p, pies, hjust=-.06)

pies_and_bars <- bars2
pies_and_bars[9:14] <- pies[9:14]
inset(p, pies_and_bars)

d <- lapply(1:15, rnorm, n=100)
ylim <- range(unlist(d))
bx <- lapply(d, function(y) {
    dd <- data.frame(y=y)
    ggplot(dd, aes(x=1, y=y))+geom_boxplot() + ylim(ylim) + theme_inset()
})
names(bx) <- 1:15
inset(p, bx, width=.06, height=.2, hjust=-.05)

p2 <- inset(p, bars2, x='branch', width=.06, vjust=-.4)
p2 <- inset(p2, pies, x='branch', vjust=.4)
bx2 <- lapply(bx, function(g) g+coord_flip())
inset(p2, bx2, width=.4, height=.06, vjust=.04, hjust=p2$data$x[1:15]-4) + xlim(NA, 4.5)

Annotate with image files

imgfile <- tempfile(, fileext=".png")
download.file("https://avatars1.githubusercontent.com/u/626539?v=3&u=e731426406dd3f45a73d96dd604bc45ae2e7c36f&s=140", destfile=imgfile, mode='wb')
img <- list(imgfile, imgfile)
names(img) <- c("18", "22")
inset(p, img)

Plot tree with associated data

For associating phylogenetic tree with different type of plot produced by user’s data, ggtree provides facet_plot function which accepts an input data.frame and a geom function to draw the input data. The data will be displayed in an additional panel of the plot.

tr <- rtree(30)

d1 <- data.frame(id=tr$tip.label, val=rnorm(30, sd=3))
p <- ggtree(tr)

p2 <- facet_plot(p, panel="dot", data=d1, geom=geom_point, aes(x=val), color='firebrick')
d2 <- data.frame(id=tr$tip.label, value = abs(rnorm(30, mean=100, sd=50)))

facet_plot(p2, panel='bar', data=d2, geom=geom_segment, aes(x=0, xend=value, y=y, yend=y), size=3, color='steelblue') + theme_tree2()

Tree annotation with Phylopic

PhyloPic is a database that stores reusable silhouette images of organisms. ggtree supports downloading images from PhyloPic and annotating phylogenetic tree with the downloaded images.

pp <- ggtree(tree) %>% phylopic("79ad5f09-cf21-4c89-8e7d-0c82a00ce728", color="steelblue", alpha = .3)
print(pp)

pp %>% phylopic("67382184-5135-4faa-8e98-eadff02c3e8a", color="#86B875", alpha=.8, node=4) %>%
     phylopic("d3563b54-780f-4711-a49a-7ea051e9dacc", color="darkcyan", alpha=.8, node=17, width=.2)