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

• Homepage: bioconductor.org/packages/tanggle
• Vignette: https://bioconductor.org/packages/release/bioc/vignettes/tanggle/inst/doc/tanggle.html