A Fast, Flexible Tool for Sorting Phylogenetic Trees

Description

PhySortR provides a quick and highly flexible function for the screening (within a tree) of Exclusive clades that comprise only the target taxa and/or Non-Exclusive clades that includes a defined portion of non-target taxa. Support is also provided for both traditional and extended Newick formatted phylogenetic trees.

A full list of functions can be displayed by library(help = PhySortR).

Details

Author(s)

Timothy G. Stephens, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan

Maintainer: Timothy G. Stephens <timothy.stephens1@uqconnect.edu.au>

References

Stephens TG, Bhattacharya D, Ragan MA, Chan CX. 2016. PhySortR: a fast, flexible tool for sorting phylogenetic trees in R. PeerJ, 4:e2038, DOI:10.7717/peerj.2038

Converts Extended Newick Format to Traditional Newick Format

Description

Takes a phylogenetic tree in extended Newick format and converts it to traditional Newick format that can be directly manipulated by packages such as ape and phytools.

Usage

convert.eNewick(eNewick)

Arguments

Value

phylogenetic tree in traditional Newick format.

Examples

 ### Converts the phylogenetic tree into traditional Newick format. 
 tree <- "((A:0.1,(B:0.3,C:0.2):0.2[60]):0.4[100],(E:0.12,F:0.09):0.4[100]);"
 new.tree <- convert.eNewick(tree)
 new.tree

Sorts Phylogenetic Trees using Taxa Identifiers

Description

Reads phylogenetic trees from a directory and sorts them based on the presence of Exclusive and Non-Exclusive clades containing a set of given target leaves at a desired support value. Can interpret trees in both Newick and extended Newick format.

Usage

sortTrees(
  target.groups,
  min.support = 0,
  min.prop.target = 0.7,
  in.dir = ".",
  out.dir = "Sorted_Trees",
  mode = "l",
  clades.sorted = "E,NE",
  extension = ".tre",
  clade.exclusivity = 0.9
)

Arguments

Value

Will always return a list containing the names of the trees identified during sorting, irrespective of the mode argument.

Examples

 ### Load data ###
 extdata <- system.file("extdata", package="PhySortR")
 file.copy(dir(extdata, full.names = TRUE), ".")
 dir.create("Algae_Trees/")
 file.copy(dir(extdata, full.names = TRUE), "Algae_Trees/")
 
 ### Examples ###
 # (1) Sorting using 3 target terms, all other parameters default. 
 sortTrees(target.groups = "Rhodophyta,Viridiplantae")
 
 # The function will search in the users current working directory for files 
 # with the extension ".tre" and check them (using default min.support, 
 # min.prop.target and clade.exclusivity) for Exclusive, All Exclusive or 
 # Non-Exclusive clades. A list will be returned with the names of the trees 
 # identified during sorting. 
 
 
 
 # (2) Sorting with a target directory and an out directory specified.
 sortTrees(target.groups = "Rhodophyta,Viridiplantae",
   in.dir= "Algae_Trees/", 
   out.dir="Sorted_Trees_RVG/", 
   mode = "c")
   
 # The function will search in "Algae_Trees/" for files with the extension
 # ".tre" and check them (using default min.support, min.prop.target, 
 # clade.exclusivity) for Exclusive, All Exclusive or Non-Exclusive clades. 
 # The function will both (a) return a list of the trees identified during 
 # sorting and (b) copy the files into their respective subdirectories of
 # "Algae_Trees/Sorted_Trees_RVG/Exclusive/", 
 # "Algae_Trees/Sorted_Trees_RVG/Exclusive/All_Exclusive/" and 
 # "Algae_Trees/Sorted_Trees_RVG/Non_Exclusive/".
 
 
 
 # (3) Sorting with in/out directories, min.prop.target and min.support specified.
 sortTrees(target.groups = "Rhodophyta,Viridiplantae",
   min.prop.target = 0.8,
   min.support = 90,
   in.dir= "Algae_Trees/",
   out.dir="Sorted_Trees_RVG_95/",
   mode = "c",
   clades.sorted = "NE",
   clade.exclusivity = 0.95)
   
 # The function will search in "Algae_Trees/" for files with the 
 # extension ".tre" and check them for only Non-Exclusive clades. 
 # A clade will only be defined if it has support >= 90 and contains at least
 # 80% of the total target leaves in the tree. A Non-Exclusive clade must also
 # be composed of >= 95% target taxa (i.e. < 5% non-target taxa).
 # The function will (a) return a list of the trees identified during 
 # sorting and (b) copy the trees identified during sorting to the out 
 # directory "Algae_Trees/Sorted_Trees_RVG/Non_Exclusive/".
 
 # (4) Sorting with multiple min.support values specified.
 #sortTrees(target.groups = "Rhodophyta,Viridiplantae",
 #  min.prop.target = 0.8,
 #  min.support = c(75, 90),
 #  in.dir= "Algae_Trees/",
 #  out.dir="Sorted_Trees_RVG_75_95/",
 #  mode = "c",
 #  clades.sorted = "NE",
 #  clade.exclusivity = 0.95)
 
 # The function will search in "Algae_Trees/" for files with the 
 # extension ".tre" and check them for only Non-Exclusive clades. 
 # A clade will only be defined if it has its first support >= 75
 # and its second support >= 90 and contains at least 80% of the 
 # total target leaves in the tree. A Non-Exclusive clade must also
 # be composed of >= 95% target taxa (i.e. < 5% non-target taxa).
 # The function will (a) return a list of the trees identified during 
 # sorting and (b) copy the trees identified during sorting to the out 
 # directory "Algae_Trees/Sorted_Trees_RVG/Non_Exclusive/".
 
 ### Clean up ###
 unlink("Algae_Trees", recursive=TRUE)
 unlink("Sorted_Trees.log")
 unlink(dir(".", ".*.tre$"))