| name | bioconductor-tanggle |
| description | Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. 'ggtree' and using functions from 'ape' and 'phangorn'. It extends the 'ggtree' package [@Yu2017] to allow the visualization of phylogenetic networks using the 'ggplot2' syntax. It offers an alternative to the plot functions already available in 'ape' Paradis and Schliep (2019) <doi:10.1093/bioinformatics/bty633> and 'phangorn' Schliep (2011) <d |
tanggle
Workflows
Standard Workflow
Visualize unrooted, undirected split networks (such as consensus networks or neighbor-nets) from Nexus files.
library(tanggle)
library(phangorn)
library(ggtree)
fdir <- system.file("extdata/trees", package = "phangorn")
Nnet <- phangorn::read.nexus.networx(file.path(fdir,"woodmouse.nxs"))
p <- ggsplitnet(Nnet) + geom_tiplab2()
p <- p + xlim(-0.019, .003) + ylim(-.01, .012)
Input: A Nexus file containing split network data, read as a networx object; Output: A ggplot object representing the unrooted split network with tip labels.
Explicit Networks
Visualize explicit, rooted phylogenetic networks with reticulations from extended Newick format.
library(tanggle)
library(ape)
z <- read.evonet(text = "((1,((2,(3,(4)Y#H1)g)e,(((Y#H1,5)h,6)f)X#H2)c)a, ((X#H2,7)d,8)b)r;")
p <- ggevonet(z, layout = "slanted") + geom_tiplab() + geom_nodelab()
Input: An extended Newick format string; Output: A ggplot object representing a rooted phylogenetic network with reticulations.
When to Use
- Visualizing unrooted, undirected split networks (consensus networks or neighbor-nets) using
ggsplitnet.
- Visualizing explicit, rooted phylogenetic networks with reticulations using
ggevonet.
- Customizing phylogenetic network plots with
ggplot2 layers such as geom_tiplab2 and geom_nodepoint.
When NOT to Use
- For standard, non-reticulated phylogenetic trees, use
ggtree directly as it is optimized for simple tree structures.
- For plotting networks without a phylogenetic context (e.g., protein-protein interaction networks), use
ggraph or igraph.
Data Requirements
- Split networks must be represented as a
networx object, typically read via phangorn::read.nexus.networx.
- Explicit networks must be represented as an
evonet object, typically read via ape::read.evonet.
Key Parameters
- layout ("rectangular"): Layout style for explicit networks in
ggevonet (can be "rectangular" or "slanted").
- col ("blue"): Color parameter inside
geom_tiplab2 or geom_nodepoint to customize labels and nodes.
- font (4): Font style parameter in
geom_tiplab2.
- hjust (-0.15): Horizontal adjustment for tip labels in
geom_tiplab2.
Best Practices
- Adjust plot limits using
xlim and ylim to ensure long tip labels are fully visible and readable.
- Use
geom_tiplab2 for split networks to properly align labels along the network perimeter.
- Minimize reticulation line crossings in complex explicit networks using
minimize_overlap.
Common Pitfalls
- Truncated tip labels: Labels extending beyond the default plot margins. Fix by adding
xlim and ylim limits to the ggplot object.
- Overlapping reticulation lines: Hard-to-read explicit networks. Fix by applying
minimize_overlap to the network object before plotting.
Alternatives
ape: For basic plotting of evonet objects without ggplot2 syntax.phangorn: For basic plotting of networx split networks without ggplot2 integration.
Citations
- Yu, Guangchuang, David Smith, Huachen Zhu, Yi Guan, and Tommy Tsan-Yuk Lam. 2017. "Ggtree: An R Package for Visualization and Annotation of Phylogenetic Trees with Their Covariates and Other Associated Data." Methods in Ecology and Evolution 8 (1): 28–36.
- Cardona, Gabriel, Francesc Rosselló, and Gabriel Valiente. 2008. "Extended Newick: It Is Time for a Standard Representation of Phylogenetic Networks." BMC Bioinformatics 9 (1): 532.
References
