Tree Manipulation

Internal node number

Some of the functions in ggtree work with clade and accept a parameter of internal node number. To get the internal node number, user can use geom_text2 to display it:

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()

Another way to get the internal node number is using MRCA() function by providing a vector of taxa names. The function will return node number of input taxa’s most recent commond ancestor (MRCA). It works with tree and graphic object.

MRCA(tree, tip=c('A', 'E'))

## [1] 17

MRCA(tree, tip=c('H', 'G'))

## [1] 21

p <- ggtree(tree)
MRCA(p, tip=c('A', 'E'))

## [1] 17

view Clade

ggtree provides a function viewClade to visualize a clade of a phylogenetic tree.

viewClade(p+geom_tiplab(), node=21)

group Clades

The ggtree package defined several functions to manipulate tree view. groupClade and groupOTU methods were designed for clustering clades or related OTUs. groupClade accepts an internal node or a vector of internal nodes to cluster clade/clades.

Both groupClade and groupOTU work fine with tree and graphic object.

tree <- groupClade(tree, node=21)
ggtree(tree, aes(color=group, linetype=group))

The following command will produce the same figure.

ggtree(read.tree(nwk)) %>% groupClade(node=21) + aes(color=group, linetype=group)

With groupClade and groupOTU, it’s easy to highlight selected taxa and easy to select taxa to display related features.

tree <- groupClade(tree, node=c(21, 17))
ggtree(tree, aes(color=group, linetype=group)) + geom_tiplab(aes(subset=(group==2)))

group OTUs

groupOTU accepts a vector of OTUs (taxa name) or a list of OTUs. groupOTU will trace back from OTUs to their most recent common ancestor and cluster them together. Related OTUs are not necessarily within a clade, they can be monophyletic (clade), polyphyletic or paraphyletic.

tree <- groupOTU(tree, focus=c("D", "E", "F", "G"))

ggtree(tree, aes(color=group)) + geom_tiplab()

groupOTU can also input a list of tip groups.

cls <- list(c1=c("A", "B", "C", "D", "E"),
            c2=c("F", "G", "H"),
            c3=c("L", "K", "I", "J"),
            c4="M")

tree <- groupOTU(tree, cls)
library("colorspace")
ggtree(tree, aes(color=group, linetype=group)) + geom_tiplab() +
     scale_color_manual(values=c("black", rainbow_hcl(4))) + theme(legend.position="right")

groupOTU also work with graphic object.

p <- ggtree(tree)
groupOTU(p, LETTERS[1:5]) + aes(color=group) + geom_tiplab() + scale_color_manual(values=c("black", "firebrick"))

The following example use groupOTU to display taxa classification.

library("ape")
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))

collapse clade

With collapse function, user can collapse a selected clade.

cp <- ggtree(tree) %>% collapse(node=21)
cp + geom_point2(aes(subset=(node == 21)), size=5, shape=23, fill="steelblue")

expand collapsed clade

The collapsed clade can be expanded via expand function.

cp %>% expand(node=21)

p1 <- ggtree(tree)
p2 <- collapse(p1, 21) + geom_point2(aes(subset=(node==21)), size=5, shape=23, fill="blue")
p3 <- collapse(p2, 17) + geom_point2(aes(subset=(node==17)), size=5, shape=23, fill="red")
p4 <- expand(p3, 17)
p5 <- expand(p4, 21)

multiplot(p1, p2, p3, p4, p5, ncol=5)

scale clade

Collpase selected clades can save some space, another approach is to zoom out clade to a small scale.

multiplot(ggtree(tree) + geom_hilight(21, "steelblue"),
          ggtree(tree) %>% scaleClade(21, scale=0.3) + geom_hilight(21, "steelblue"),
          ncol=2)

Of course, scaleClade can accept scale larger than 1 and zoom in the selected portion.

multiplot(ggtree(tree) + geom_hilight(17, fill="steelblue") +
                 geom_hilight(21, fill="darkgreen"),
          ggtree(tree) %>% scaleClade(17, scale=2) %>% scaleClade(21, scale=0.3) +
                 geom_hilight(17, "steelblue") + geom_hilight(21, fill="darkgreen"),
          ncol=2)

rotate clade

A selected clade can be rotated by 180 degree using rotate function.

tree <- groupClade(tree, c(21, 17))
p <- ggtree(tree, aes(color=group)) + scale_color_manual(values=c("black", "firebrick", "steelblue"))
p2 <- rotate(p, 21) %>% rotate(17)
multiplot(p, p2, ncol=2)

flip clade

The positions of two selected clades (should share a same parent) can be flip over using flip function.

multiplot(p, flip(p, 17, 21), ncol=2)