Here we present a vignette for the R package tanggle, and provide an overview of its functions and their usage. Tanggle extends the ggtree R package (Yu et al. 2017) to allow for the visualization of several types of phylogenetic networks using the ggplot2 (Wickham 2016) syntax. More specifically, tanggle contains functions to allow the user to effectively plot: (1) split (i.e. implicit) networks (unrooted, undirected) and (2) explicit networks (rooted, directed) with reticulations. It offers an alternative to the plot functions already available in ape (Paradis and Schliep 2018) and phangorn (Schliep 2011).
|Function name||Brief description|
||Adds a splitnet layer to a ggplot, to combine visualising data and the network|
||Plots an explicit network from a phylo object|
||Plots an implicit network from a phylo object|
||Reduces the number of reticulation lines crossing over in the plot|
||Returns the depths or heights of nodes and tips in the phylogenetic network|
Install the package from Bioconductor directly:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("tanggle")
Or install the development version of the package from Github.
if (!requireNamespace("remotes", quietly=TRUE)) install.packages("remotes") remotes::install_github("KlausVigo/tanggle")
If you need to install ggtree from github:
And load all the libraries:
library(tanggle) library(phangorn) library(ggtree)
Split networks are data-display objects which allow for the definition of 2 (or
more) options for non-compatible splits. Split networks are most often used to
visualize consensus networks (Holland et al. 2004) or neighbor-nets
(Bryant and Moulton 2004). This can be done either by using the
neighbor-net functions in phangorn (Schliep 2011) or by importing
nexus files from SplitsTree (Huson and Bryant 2006).
tanggle accepts three forms of input data for split networks. The following input options all generate a networx object for plotting.
Read in a split network in nexus format:
fdir <- system.file("extdata/trees", package = "phangorn") Nnet <- phangorn::read.nexus.networx(file.path(fdir,"woodmouse.nxs"))
read.treeA consensus split network is then computed using the function
consensusNetin phangorn (Schliep 2011).
read.phyDatin phangorn (Schliep 2011) or the function
read.dnain ape (Paradis and Schliep 2018). Distances matrices are then computed for specific models of evolution using the function
dist.mlin phangorn (Schliep 2011) or
dist.dnain ape (Paradis and Schliep 2018). From the distance matrix, a split network is reconstructed using the function
neighborNetin phangorn (Schliep 2011). Optional: branch lengths may be estimated using the function
splitsNetworksin phangorn (Schliep 2011).
We can plot the network with the default options:
p <- ggsplitnet(Nnet) + geom_tiplab2() p
When we can set the limits for the x and y axis so that the labels are readable.
p <- p + xlim(-0.019, .003) + ylim(-.01,.012) p
You can rename tip labels. Here we changed the names to species from 1 to 15:
Nnet$translate$label <- seq_along(Nnet$tip.label)
We can include the tip labels with
geom_tiplab2, and customize some of the
options. For example, here the tip labels are in blue and both in bold and
italics, and we show the internal nodes in green:
ggsplitnet(Nnet) + geom_tiplab2(col = "blue", font = 4, hjust = -0.15) + geom_nodepoint(col = "green", size = 0.25)