Package: phylepic 0.2.1.9000

Carl Suster

phylepic: 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) <doi:10.1101/2024.04.02.24305229>.

Authors:Carl Suster [aut, cre], Western Sydney Local Health District, NSW Health [cph]

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phylepic.pdf |phylepic.html✨
phylepic/json (API)
NEWS

# Install 'phylepic' in R:

install.packages('phylepic', repos = c('https://cidm-ph.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/cidm-ph/phylepic/issues

Pkgdown site:https://cidm-ph.github.io

On CRAN:

genomics genomics-visualization public-health

4.65 score 4 scripts 459 downloads 24 exports 58 dependencies

Last updated 25 days agofrom:3d59bc4586. Checks:7 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 10 2025
R-4.5-win	OK	Jan 10 2025
R-4.5-linux	OK	Jan 10 2025
R-4.4-win	OK	Jan 10 2025
R-4.4-mac	OK	Jan 10 2025
R-4.3-win	OK	Jan 10 2025
R-4.3-mac	OK	Jan 10 2025

Exports:breaks_cached coord_tree CoordTree create_tree_layout drop.clade geom_calendar geom_node_text_filled GeomCalendar GeomTextFilled oob_infinite phylepic plot_bars plot_calendar plot_epicurve plot_tree scale_x_week stat_bin_2d_auto stat_bin_auto stat_bin_location stat_bin2d_auto StatBin2dAuto StatBinAuto StatBinLocation week_breaks

Dependencies:ape cachem cli colorspace cowplot cpp11 digest dplyr fansi farver fastmap forcats generics ggforce ggnewscale ggplot2 ggraph ggrepel glue graphlayouts gridExtra gtable igraph isoband labeling lattice lifecycle magrittr MASS Matrix memoise mgcv munsell nlme pillar pkgconfig polyclip purrr R6 RColorBrewer Rcpp RcppArmadillo RcppEigen rlang scales stringi stringr systemfonts tibble tidygraph tidyr tidyselect tweenr utf8 vctrs viridis viridisLite withr

phylepic charts: combining phylogenetic trees with epidemic curves

Rendered fromphylepic.Rmdusingknitr::rmarkdownon Jan 10 2025.

Last update: 2025-01-09
Started: 2024-04-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Cached scale break function	breaks_cached
Cartesian coordinates with specialised grid for trees	CoordTree coord_tree
Create a graph layout for plotting	create_tree_layout
Drop a clade from a phylogentic tree	drop.clade
Annotate nodes with text and a background	GeomTextFilled geom_node_text_filled
Specialised rectangular geometry for calendar plots	GeomCalendar geom_calendar
Out of bounds handling	oob_infinite
Combine metadata (a line list) with a phylogenetic tree	phylepic
Plot metadata bars panel	plot_bars
Plot calendar panel	plot_calendar
Plot epidemic curve panel	plot_epicurve
Plot phylogenetic tree panel	plot_tree
Plot "phylepic" objects	autoplot.phylepic plot.phylepic
Date scale with breaks specified by week	scale_x_week
Calculate two-dimensional bins using scale breaks	StatBin2dAuto stat_bin2d_auto stat_bin_2d_auto
Calculate bins using scale breaks	StatBinAuto stat_bin_auto
Annotate rows with 2D bin positions	StatBinLocation stat_bin_location
Breaks for week-binning date axes	week_breaks