Layers that allows subsetting
Subsetting is not supported in layers defined in ggplot2, while it is quite useful in phylogenetic annotation since it allows us to annotate at specific node(s).
In ggtree, we provides modified version of layers defined in ggplot2 to support subsetting, including:
- geom_segment2
- geom_point2
- geom_text2
- geom_label2
file <- system.file("extdata/BEAST", "beast_mcc.tree", package="treeio")
beast <- read.beast(file)
ggtree(beast) + geom_point2(aes(subset=!is.na(posterior) & posterior > 0.75), color='firebrick')
Multiple graphs on one page
To support viewing multiple plots, ggtree provides multiplot function that similar to gridExtra::grid.arrange with extra feature of labeling the plots.
subplots in ggplot object
ggtree implemented a function, subview, that can add subplots on a ggplot2 object.
set.seed(2016-01-04)
tr <- rtree(30)
tr <- groupClade(tr, node=45)
p <- ggtree(tr, aes(color=group)) + geom_tippoint()
p1 <- p + geom_hilight(node=45)
p2 <- viewClade(p, node=45) + geom_tiplab()
subview(p2, p1+theme_transparent(), x=2.3, y=28.5)
This is the backend of the inset function.
This subview function works with any ggplot objects and it had successful applied to plot pie graphs on map.
library(ggtree)
dd <- data.frame(x=LETTERS[1:3], y=1:3)
pie <- ggplot(dd, aes(x=1, y, fill=x)) + geom_bar(stat="identity", width=1) + coord_polar(theta="y") + theme_inset()
x <- sample(2:9)
y <- sample(2:9)
width <- sample(seq(0.05, 0.15, length.out=length(x)))
height <- width
p <- ggplot(data=data.frame(x=c(0, 10), y=c(0, 10)), aes(x, y))+geom_blank()
for (i in seq_along(x)) {
p <- subview(p, pie, x[i], y[i], width[i], height[i])
print(p)
}