feature request: phylo4d compatibility about ggtree

[ashenkin]

This is great! Thanks so much. It seems to work. Here's an example of adding node colors too. I think this is a very nice step forward for your very nice package.

require(ggtree)

set.seed(123)
tr = rtree(30)
g1 = as(tr, 'phylo4')
d = data.frame(color=sample(c('red', 'blue', 'green'), 30, replace=T))
rownames(d) = tr$tip.label
g2 = phylo4d(g1, d)

ggtree(g2) + geom_tippoint(aes(color=I(color)))

rNodeData <- data.frame(randomTrait = rnorm(nNodes(g1)),
                        color = sample(c('purple', 'yellow', 'black'), nNodes(g1), replace=T),
                        row.names = nodeId(g1, "internal"))

nodeData(g2) <- rNodeData

ggtree(g2) + geom_tippoint(aes(color=I(color))) + geom_nodepoint(aes(size = randomTrait, color = I(color)))

[GuangchuangYu]

require(phylobase)
require(ggtree)

set.seed(123)
tr = rtree(30)
g1 = as(tr, 'phylo4')
d = data.frame(color=sample(c('red', 'blue', 'green'), 30, replace=T))
rownames(d) = tr$tip.label
g2 = phylo4d(g1, d)

ggtree(g2) + geom_tippoint(aes(color=I(color)))

it was supported in ggtree >= 1.5.2

[GuangchuangYu]

thanks for your feedback 👍

[GuangchuangYu]

it can be done using %<+% operator to attach user's data.

require(ggtree)

set.seed(123)
tr = rtree(30)
g1 = as(tr, 'phylo4')
d = data.frame(lab=tr$tip.label, color=sample(c('red', 'blue', 'green'), 30, replace=T))

p <- ggtree(g1) %<+% d + geom_tippoint(aes(color=I(color)))

rNodeData <- data.frame(node = nodeId(g1, "internal"), 
                        randomTrait = rnorm(nNodes(g1)),
                        color2 = sample(c('purple', 'yellow', 'black'), nNodes(g1), replace=T)
                        )


p %<+% rNodeData  + geom_nodepoint(aes(size = randomTrait, color = I(color2)))

This phylo4d solution is a very good alternative.

In ggtree, we also provide another solution, that is to merge the newick tree text with user's data to a single jplace file and then parse the file in ggtree and visualize it with user's data.