https://github.com/cidm-ph/phylepic

Epidemic curve + phylogenomic tree
https://github.com/cidm-ph/phylepic

genomics genomics-visualization public-health r

Last synced: about 1 month ago
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Epidemic curve + phylogenomic tree

• Host: GitHub
• URL: https://github.com/cidm-ph/phylepic
• Owner: cidm-ph
• License: other
• Created: 2024-03-11T05:49:08.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2025-07-02T00:35:18.000Z (4 months ago)
• Last Synced: 2025-09-06T04:25:43.499Z (about 1 month ago)
• Topics: genomics, genomics-visualization, public-health, r
• Language: R
• Homepage: https://cidm-ph.github.io/phylepic/
• Size: 16.4 MB
• Stars: 1
• Watchers: 2
• Forks: 1
• 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%"

)

```

# phylepic

[![r-universe status](https://cidm-ph.r-universe.dev/badges/phylepic)](https://cidm-ph.r-universe.dev)

[![R-CMD-check](https://github.com/cidm-ph/phylepic/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/cidm-ph/phylepic/actions/workflows/R-CMD-check.yaml)

[![CRAN

status](https://www.r-pkg.org/badges/version/phylepic)](https://CRAN.R-project.org/package=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:

``` r

# 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.

```{r example, fig.width=7, fig.height=4, eval = F}

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](https://cidm-ph.github.io/phylepic/articles/phylepic.html) 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](https://doi.org/10.1017/S0950268824001092),