(This article was first published on R on Guangchuang YU, and kindly contributed to R-bloggers)
With ggimage, we are able to plot images using grammar of graphics. The layers defined in ggimage can be directly applied to ggtree to annotate phylogenetic tree using local/online image files.
ggtree seamlessly work with ggimage. The geom_tiplab and geom_nodelab can accept parameter of geom="image" to parse taxa labels as image files and use them to “label” the taxa using images instead of text strings. Here are some examples for demonstration.
Annotate tips
library(ggimage)library(ggtree)url <- paste0("https://raw.githubusercontent.com/TreeViz/", "metastyle/master/design/viz_targets_exercise/")x <- read.tree(paste0(url, "tree_boots.nwk"))info <- read.csv(paste0(url, "tip_data.csv"))p <- ggtree(x) %<+% info + xlim(NA, 6)p + geom_tiplab(aes(image= imageURL), geom="image", offset=2, align=T, size=.16, hjust=0) + geom_tiplab(geom="label", offset=1, hjust=.5)
Annotate internal nodes
## example from https://rgriff23.github.io/2017/05/11/primate-phylogeny-ggtree.htmllibrary(ape)tree <- read.nexus("https://raw.githubusercontent.com/rgriff23/Dissertation/master/Chapter_2/data/tree.nex")phylopic_info <- data.frame(node = c(124, 113, 110, 96, 89, 70), phylopic = c("7fb9bea8-e758-4986-afb2-95a2c3bf983d", "bac25f49-97a4-4aec-beb6-f542158ebd23", "f598fb39-facf-43ea-a576-1861304b2fe4", "aceb287d-84cf-46f1-868c-4797c4ac54a8", "0174801d-15a6-4668-bfe0-4c421fbe51e8", "72f2f854-f3cd-4666-887c-35d5c256ab0f"), species = c("galagoids", "lemurs", "tarsiers", "cebids", "hominoids", "cercopithecoids"))pg <- ggtree(tree)pg %<+% phylopic_info + geom_nodelab(aes(image=phylopic), geom="phylopic", alpha=.5, color='steelblue')
d <- data.frame(node = c("70","89","96","110","113","124"), images = c("https://i.imgur.com/8VA9cYw.png", "https://i.imgur.com/XYM1T2x.png", "https://i.imgur.com/EQs5ZZe.png", "https://i.imgur.com/2xin0UK.png", "https://i.imgur.com/hbftayl.png", "https://i.imgur.com/3wDHW8n.png"))pg %<+% d + geom_nodelab(aes(image=images), geom="image")
Use image as background
pg + geom_phylopic(image="79ad5f09-cf21-4c89-8e7d-0c82a00ce728", size=Inf, alpha=.5, color='firebrick')
Here is another example that uses Tabikaeru (known as traveling frog, a popular mobile game) image to decorate a phylogenetic tree of frog, see reproducible source code on https://github.com/GuangchuangYu/frog_tree.
To leave a comment for the author, please follow the link and comment on their blog: R on Guangchuang YU.
R-bloggers.com offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...