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:
phylepic_0.2.1.9000.tar.gz
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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
genomicsgenomics-visualizationpublic-health
Last updated 2 months agofrom:3d59bc4586. Checks:6 OK, 3 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 11 2025 |
| R-4.5-win | NOTE | Mar 11 2025 |
| R-4.5-mac | NOTE | Mar 11 2025 |
| R-4.5-linux | NOTE | Mar 11 2025 |
| R-4.4-win | OK | Mar 11 2025 |
| R-4.4-mac | OK | Mar 11 2025 |
| R-4.4-linux | OK | Mar 11 2025 |
| R-4.3-win | OK | Mar 11 2025 |
| R-4.3-mac | OK | Mar 11 2025 |
Exports:breaks_cachedcoord_treeCoordTreecreate_tree_layoutdrop.cladegeom_calendargeom_node_text_filledGeomCalendarGeomTextFilledoob_infinitephylepicplot_barsplot_calendarplot_epicurveplot_treescale_x_weekstat_bin_2d_autostat_bin_autostat_bin_locationstat_bin2d_autoStatBin2dAutoStatBinAutoStatBinLocationweek_breaks
Dependencies:apecachemclicolorspacecowplotcpp11digestdplyrfansifarverfastmapforcatsgenericsggforceggnewscaleggplot2ggraphggrepelgluegraphlayoutsgridExtragtableigraphisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmunsellnlmepillarpkgconfigpolyclippurrrR6RColorBrewerRcppRcppArmadilloRcppEigenrlangscalesstringistringrsystemfontstibbletidygraphtidyrtidyselecttweenrutf8vctrsviridisviridisLitewithr
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 |
