Combined Visualisation of Phylogenetic and Epidemiological Data

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) .

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:

# CRAN release
install.packages('phylepic')

# 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.” Epidemiology & Infection 152: e110. doi:10.1017/S0950268824001092,