Description
Combined Visualisation of Phylogenetic and Epidemiological Data.
Description
A collection of utilities and 'ggplot2' extensions to assist with visualisations in genomic epidemiology. This includes the 'phylepic' chart, a visual combination of a phylogenetic tree and a matched epidemic curve. The included 'ggplot2' extensions such as date axes binned by week are relevant for other applications in epidemiology and beyond. The approach is described in Suster et al. (2024) <doi:10.1101/2024.04.02.24305229>.
README.md
phylepic
Phylepic contains tools for visualisations that are useful for genomic epidemiology of pathogens, designed for a public health setting.
Installation
You can install phylepic like so:
# development version
install.packages('phylepic', repos = c('https://cidmp-ph.r-universe.dev', 'https://cloud.r-project.org'))
Example
This is an example of a very minimal phylepic chart.
library(ape)
library(phylepic)
tree <- read.tree(text = "((D:0.3,C:0.4):0.5,B:0.1,A:0.2);")
metadata <- data.frame(
ID = c("A", "B", "C", "D"),
date = as.Date(c("2024-01-10", "2024-01-12", "2024-01-21", "2024-01-23")),
country = factor(c("Australia", "Australia", NA, "New Zealand"))
)
phylepic(tree, metadata, ID, date) |> plot()
Refer to the package vignette for a more complete example.
Citation
See citation("phylepic").
Suster CJE, Watt AE, Wang Q, Chen SC, Kok J, Sintchenko V (2024). “Combined visualization of genomic and epidemiological data for outbreaks [Preprint].” medRxiv. doi:10.1101/2024.04.02.24305229,