Chapter 11 Other ggtree extensions

rp <- BiocManager::repositories()
db <- utils::available.packages(repo=rp)
x <- tools::package_dependencies('ggtree', db=db, 
                                which = c("Depends", "Imports"), 
                                reverse=TRUE)
print(x)                                

## $ggtree
## [1] "LINC"              "LymphoSeq"        
## [3] "MicrobiotaProcess" "philr"            
## [5] "singleCellTK"      "universalmotif"   
## [7] "genBaRcode"        "harrietr"         
## [9] "STraTUS"

There are 9 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
• microbiomeViz: Visualize microbiome data with black magic ggtree
• microbiomeMarker

11.1 Taxonomy annotation using MicrobiotaProcess