Annotate a phylogenetic tree with insets

ggtree implemented a function, subview, that can add subplots on a ggplot2 object. It had successful applied to plot pie graphs on map.

set.seed(2016-01-04)
tr <- rtree(30)
tr <- groupClade(tr, node=45)
p <- ggtree(tr, aes(color=group)) + geom_tippoint()
cpos <- get_clade_position(p, node=45)
p1 <- p + geom_hilight(node=45)
p2 <- with(cpos, p+xlim(xmin, xmax*1.01)+ylim(ymin, ymax))
with(cpos, subview(p2+geom_tiplab(), p1+theme_transparent(), x=xmin+(xmax-xmin)*.15, y=ymin+(ymax-ymin)*.85))

To make it more easy to use subview function for annotating taxa with subplots, 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.

Annotate with 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)


The sizes of the insets can be ajusted by the paramter width and height.

inset(p, bars, width=.03, height=.06)


Users can set the color via the parameter color. The x position can be one of ‘node’ or ‘branch’ and can be adjusted by the parameter hjust and vjust for horizontal and vertical adjustment respecitvely.

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=.03, vjust=-.3)
print(p2)

Annotate with pie charts

Similarly, users can use nodepie function to generate a list of pie charts and place these charts to annotate corresponding nodes. Both nodebar and nodepie accepts parameter alpha to allow transparency.

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

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

Annotate with other types of charts

The inset function accepts a list of ggplot graphic objects and these input objects are not restricted to pie or bar charts. They can be any kinds of charts and hybrid of these charts.

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=.03, height=.1, hjust=-.05)

After annotating with insets, users can further annotate the tree with another layer of insets.

p2 <- inset(p, bars2, x='branch', width=.03, vjust=-.4)
p2 <- inset(p2, pies, x='branch', vjust=.4)
bx2 <- lapply(bx, function(g) g+coord_flip())
inset(p2, bx2, width=.2, height=.03, vjust=.04, hjust=p2$data$x[1:15]-4) + xlim(NA, 4.5)

Citation

G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. doi:10.1111/2041-210X.12628.

Plea to against BMC
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