Package: phylepic 0.2.0
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:
phylepic_0.2.0.tar.gz
phylepic_0.2.0.tar.gz(r-4.5-noble)phylepic_0.2.0.tar.gz(r-4.4-noble)
phylepic_0.2.0.tgz(r-4.4-emscripten)phylepic_0.2.0.tgz(r-4.3-emscripten)
phylepic.pdf |phylepic.html✨
phylepic/json (API)
NEWS
# Install 'phylepic' in R: |
install.packages('phylepic', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/cidm-ph/phylepic/issues
Last updated 3 months agofrom:5341505b5f. Checks:OK: 2. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 30 2024 |
R-4.5-linux | OK | Aug 30 2024 |
Exports:coord_treeCoordTreecreate_tree_layoutdrop.cladegeom_calendargeom_node_text_filledGeomCalendarGeomTextFilledoob_infinitephylepicplot_barsplot_calendarplot_epicurveplot_treescale_x_weekstat_weekstat_week_2dStatWeekStatWeek2dweek_breaks
Dependencies:apecachemclicolorspacecowplotcpp11digestdplyrfansifarverfastmapforcatsgenericsggforceggnewscaleggplot2ggraphggrepelgluegraphlayoutsgridExtragtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmunsellnlmepillarpkgconfigpolyclippurrrR6RColorBrewerRcppRcppArmadilloRcppEigenrlangscalesstringistringrsystemfontstibbletidygraphtidyrtidyselecttweenrutf8vctrsviridisviridisLitewithr
Readme and manuals
Help Manual
Help page | Topics |
---|---|
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 tile 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 week bins from dates | StatWeek StatWeek2d stat_week |
Calculate week bins with additional binning in the y axis | stat_week_2d |
Breaks for week-binning date axes | week_breaks |