August 30, 2015

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I implemented a function, subview, in
that make it easy to embed a subplot in ggplot.

An example is shown below:


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_tree() + 
                          xlab(NULL) + ylab(NULL) + 

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(pie, x[i], y[i], width[i], height[i])

With this function, we can plot a specific clade and add a subplot of
the whole topology; we can also add relative statistic graph above the
tree or to a specific node. It’s not specific to phylogenetic tree, it
works with all ggplot objects as demonstrated in the example.

PS: ggtree is now
presented in CRAN Task View:

AND get its first citation.

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