Chapter 12 ggtree extensions

rp <- BiocManager::repositories()
db <- utils::available.packages(repo=rp)
x <- tools::package_dependencies('ggtree', db=db, 
                                which = c("Depends", "Imports"), 
## $ggtree
## [1] "LINC"           "LymphoSeq"      "philr"         
## [4] "singleCellTK"   "universalmotif" "genBaRcode"    
## [7] "harrietr"       "STraTUS"

There are 8 packages in CRAN or Bioconductor that depend or import ggtree and several packages on github that extends ggtree.

  • deeptime: Plotting Tools for Anyone Working in Deep Time
  • ggnetworx: phylogenetic networks using ggplot2 and ggtree
  • ggdaisie: ggtree and DAISIE R package
  • MicrobiotaProcess: an package for analysis, visualization and biomarker discovery of microbiome
  • microbiomeViz: Visualize microbiome data with black magic ggtree