Returns a data table defining the line segments of a phylogenetic tree.
This function takes a phylo or phyloseq-class object
and returns a list of two data.tables suitable for plotting
a phylogenetic tree with ggplot2.
tree_layout(phy, ladderize = FALSE)
phy |
(Required). The |
ladderize |
(Optional). Boolean or character string (either
|
A list of two data.tables, containing respectively
a data.table of edge segment coordinates, named edgeDT,
and a data.table of vertical connecting segments, named vertDT.
See example below for a simple demonstration.
An early example of this functionality was borrowed directly, with permission,
from the package called ggphylo,
released on GitHub at:
https://github.com/gjuggler/ggphylo
by its author Gregory Jordan gjuggler@gmail.com.
That original phyloseq internal function, tree.layout, has been
completely replaced by this smaller and much faster user-accessible
function that utilizes performance enhancements from standard
data.table magic as well as ape-package
internal C code.
library("ggplot2")
data("esophagus")
phy = phy_tree(esophagus)
phy <- ape::root(phy, "65_2_5", resolve.root=TRUE)
treeSegs0 = tree_layout(phy)
treeSegs1 = tree_layout(esophagus)
edgeMap = aes(x=xleft, xend=xright, y=y, yend=y)
vertMap = aes(x=x, xend=x, y=vmin, yend=vmax)
p0 = ggplot(treeSegs0$edgeDT, edgeMap) + geom_segment() + geom_segment(vertMap, data=treeSegs0$vertDT)
p1 = ggplot(treeSegs1$edgeDT, edgeMap) + geom_segment() + geom_segment(vertMap, data=treeSegs1$vertDT)
print(p0)
print(p1)
plot_tree(esophagus, "treeonly")
plot_tree(esophagus, "treeonly", ladderize="left")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.