# Annotate a phylogenetic tree with insets

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`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)

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