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https://github.com/fmarotta/recphylo
Parse recPhyloXML and phyloXML files in R.
https://github.com/fmarotta/recphylo
Last synced: about 11 hours ago
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Parse recPhyloXML and phyloXML files in R.
- Host: GitHub
- URL: https://github.com/fmarotta/recphylo
- Owner: fmarotta
- License: other
- Created: 2023-11-21T17:43:58.000Z (12 months ago)
- Default Branch: main
- Last Pushed: 2024-07-28T10:15:45.000Z (4 months ago)
- Last Synced: 2024-07-28T11:51:34.013Z (4 months ago)
- Language: R
- Homepage:
- Size: 200 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.Rmd
- License: LICENSE
Awesome Lists containing this project
README
---
output: github_document
---
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# recPhylo
[](https://github.com/fmarotta/recPhylo/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/fmarotta/recPhylo?branch=main)
`recPhylo` provides a way to import simple or reconciliated phylogenies into R in a way that makes it easy to plot the trees with `ggplot2`. The starting point is an XML file following either the [phyloXML](http://www.phyloxml.org/) or the [recPhyloXML format](http://phylariane.univ-lyon1.fr/recphyloxml/), which will be parsed into specific R objects. Dedicated `layout_*()` functions can convert these objects into data.frames ready to be used with ggplot.
Contrary to `ggtree` or `ggraph`, with this package you don't get a plot directly from the tree object, but rather a pair of data.frames representing the computed layouts of nodes and edges.
It is your responsibility, then, to use the appropriate ggplot geoms (typically geom_point() or geom_line()).
The advantages of this approach are:
* We don't need to duplicate existing geoms (e.g. we don't need to wrap geom_point() inside geom_node_point(), we can simply reuse geom_point())
* We can make use of special geoms defined in other packages (e.g. geom_link2() from ggforce, without having to define a special geom for phylogeny objects)
* We have better control over the layout and annotation: the x and y coordinates of all the objects are transparently saved in the layout data.frames, so it's straightforward to add custom ggplot elements corresponding to those coordinates (e.g. a tree and a multiple sequence alignment).
* We can make use of other `ggplot2` tricks, like coord_polar(), to create new layouts "for free".
* Should you want to use a graphics package different from `ggplot2`, you can reuse the layout computed by recPhylo.
This package does not have as many features as `ggtree`. Use it if you are comfortable with `ggplot2` and like to have full control over your figures.
## Installation
You can install the development version of recPhylo from [GitHub](https://github.com/) with:
``` r
# install.packages("devtools")
devtools::install_github("fmarotta/recPhylo")
```
## Example
### recPhylo objects
This is a basic example which shows you how to plot a reconciliated phylogenetic tree.
```{r}
library(recPhylo)
library(ggplot2)
recphylo_file <- system.file("extdata", "recphylo_example_1.xml", package = "recPhylo")
recphylo_xml <- read_recPhyloXML(recphylo_file)
recphylo_layout <- layout_recphylo(recphylo_xml, branch_length_scale = 5)
ggplot() +
geom_line(data = recphylo_layout$spEdges, aes(x, y, group = group)) +
geom_line(data = recphylo_layout$recGeneEdges, aes(x, y, group = group, color = lineage, linetype = leg_type), show.legend = F) +
scale_linetype_manual(values = c("loss_vertical" = 2, "transferBack" = 3), na.value = 1) +
theme_void() +
NULL
```
### Simple phylogeny objects
Although the primary goal of the package was to plot reconciliated trees, for which there was no alternative in R, it is also possible to plot simple phylogenies.
```{r}
library(recPhylo)
library(ggplot2)
phylo_file <- system.file("extdata", "phylo_example_1.xml", package = "recPhylo")
phylo_xml <- read_phyloXML(phylo_file)[[1]]
phylo_xml <- add_annot(phylo_xml, data.frame(
name = find_descendants(phylo_xml$clade, "Bacteria"),
is_bacterium = TRUE
))
phylo_layout <- layout_phylogeny(phylo_xml, branch_length_scale = 5)
ggplot() +
geom_line(data = phylo_layout$edges, aes(x, y, group = group, color = is_bacterium)) +
theme_void() +
NULL
```
## Features
- Parse and draw phyloXML or recPhyloXML trees with ggplot2
- Three linear layouts: real branch lengths, uniform branch lengths, aligned leaves
- Corresponding circular layouts "for free" thanks to coord_polar()
- Manually adjust the space between clades
- Swap left and right children of a species node
- Swap children of a duplication event
- Import branch lengths from another species tree file
- Add custom annotation for species nodes, gene nodes, species edges, gene edges
- Convenience methods to extract data from phylogenies or decorate them with additional attributes
## Bugs and missing features
- bifurcationOut events are not supported (but planned)
- We don't automatically scale the plot to make it look nicer (planned)
- We make no attempt to minimise the edge crossings for lateral
transfers (though you can manually swap left/right children to make the tree look better)