ggplot2 now has an official extension mechanism. This means that others can now easily create their own stats, geoms and positions, and provide them in other packages. This should allow the ggplot2 community to flourish, even as less development work happens in ggplot2 itself. This page showcases these extensions.
ggiraph

Make ggplot interactive
ggstance

Horizontal versions of ggplot2 geoms
ggalt

Extra coordinate systems, geoms & stats
ggforce

Accelarating ggplot2
ggrepel

Repel overlapping text labels
ggraph

Plot graph-like data structures
ggpmisc

Miscellaneous extensions to ggplot2
geomnet

Network visualizations in ggplot2
ggExtra

Marginal density plots or histograms
gganimate

Create easy animations with ggplot2
plotROC

Interactive ROC plots
ggthemes

ggplot themes and scales
ggspectra

Extensions for radiation spectra
ggnetwork

Geoms to plot networks with ggplot2
ggtech

ggplot2 tech themes, scales, and geoms
ggradar

radar charts with ggplot2
ggTimeSeries

Time series visualisations
ggtree

A phylogenetic tree viewer
ggseas

Seasonal adjustment on the fly

ggtree

https://bioconductor.org/packages/release/bioc/html/ggtree.html

gtree is designed for visualizing phylogenetic tree and different types of associated annotation data.

# Example from https://bioconductor.org/packages/release/bioc/html/ggtree.html
library(ggplot2)
library(ape)
library(ggtree)

Tree Data Import

file <- system.file("extdata/BEAST", "beast_mcc.tree", package="ggtree")
beast <- read.beast(file)

Users can use ggtree(beast) to visualize the tree and add layer to annotate it.

ggtree(beast, ndigits=2, branch.length = 'none') + geom_text(aes(x=branch, label=length_0.95_HPD), vjust=-.5, color='firebrick')

Tree Visualization

To view a phylogenetic tree, we first need to parse the tree file into R. The ggtree package supports many file format including output files of commonly used software packages in evolutionary biology. For more details, plase refer to the Tree Data Import vignette.

library("ggtree")
nwk <- system.file("extdata", "sample.nwk", package="ggtree")
tree <- read.tree(nwk)
ggplot(tree, aes(x, y)) + geom_tree() + theme_tree()

Tree Manipulation

Internal node number

Some of the functions in ggtree works with clade and accepts a parameter of internal node number. To get the internal node number, user can use geom_text2 to display it:

nwk <- system.file("extdata", "sample.nwk", package="ggtree")
tree <- read.tree(nwk)
ggtree(tree) + geom_text2(aes(subset=!isTip, label=node), hjust=-.3) + geom_tiplab()

The following example use groupOTU to display taxa classification.

data(chiroptera)
groupInfo <- split(chiroptera$tip.label, gsub("_\\w+", "", chiroptera$tip.label))
chiroptera <- groupOTU(chiroptera, groupInfo)
ggtree(chiroptera, aes(color=group), layout='circular') + geom_tiplab(size=1, aes(angle=angle))