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ggplot2 extensions-ggtree.
The document provides a guide on using the 'ggtree' package in R for visualizing phylogenetic trees. It includes examples of how to read and plot tree data from different formats, including BEAST and Newick files. Key functions such as 'ggtree()', 'geom_tiplab()', and 'geom_text()' are demonstrated to customize tree layouts and aesthetics.
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ggplot2 extensions-ggtree.
- 1. Prepared by VolkanOBAN ggtree in R Reference: https://www.ggplot2-exts.org/ggtree.html >library("ggtree") >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))
- 2. Example: > library(ggplot2) > library(ape) >library(ggtree) > file <- system.file("extdata/BEAST", "beast_mcc.tree", package="ggtree") > beast <- read.beast(file) > ggtree(beast, ndigits=2, branch.length = 'none') + geom_text(aes(x=branch , label=length_0.95_HPD), vjust=-.5, color='firebrick')
- 3. Example: ibrary("ggtree") > nwk <-system.file("extdata", "sample.nwk", package="ggtree") > tree <- read.tree(nwk) > ggplot(tree, aes(x, y)) + geom_tree() + theme_tree()
- 4. Example: > library(ggplot2) > library(ape) >library(ggtree) 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()