Combined Visualisation of Phylogenetic and Epidemiological Data
Cached scale break function
Cartesian coordinates with specialised grid for trees
Create a graph layout for plotting
Drop a clade from a phylogentic tree
Plot metadata bars panel
Plot calendar panel
Plot epidemic curve panel
Plot phylogenetic tree panel
Plot "phylepic" objects
Date scale with breaks specified by week
Specialised rectangular geometry for calendar plots
Annotate nodes with text and a background
Out of bounds handling
phylepic: Combined Visualisation of Phylogenetic and Epidemiological D...
Combine metadata (a line list) with a phylogenetic tree
Calculate two-dimensional bins using scale breaks
Calculate bins using scale breaks
Annotate rows with 2D bin positions
Breaks for week-binning date axes
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>.
Useful links