ggtree version of plotTree
PLOTTING TREES + DATA is difficult. @DrKatHolt developed plotTree (R and Python scripts) to visualize associated data with trees, e.g. heatmap, horizontal bar etc.
I reproduced the examples presented in the plotTree repo using ggtree. Source code is freely available in https://github.com/GuangchuangYu/plotTree-ggtree.
Here are the outputs produced by
Tree with basic strain info
Pan genome heatmap
Curated genes, coloured
It can be very easy to produce a circular/fan layout version, and the tree was used to generate the ggtree hex sticker.
General solution with
ggtree provide the
facet_plot function which can be used to associate different types of data to the tree. With
ggtree we can associate more data (can be different types) and combine them freely.
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.