# Tanggle

> tanggle

- Skill: `biomate-ai/tanggle` (Agent Skill)
- Install (CLI): `npx skillmds@latest add biomate-ai/tanggle`
- Raw SKILL.md: https://api.skillmd.com/api/skills/biomate-ai/tanggle/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: biomate-ai (https://skillmd.com/u/biomate-ai)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/biomate-ai/tanggle

---


# tanggle

## Workflows

### Standard Workflow

Visualize unrooted, undirected split networks (such as consensus networks or neighbor-nets) from Nexus files.

```r
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.

```r
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