| Title: | A Fast, Flexible Tool for Sorting Phylogenetic Trees |
|---|---|
| Description: | Screens and sorts phylogenetic trees in both traditional and extended Newick format. Allows for the fast and flexible 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. |
| Authors: | Timothy Stephens [aut, cre, trl] (R port), Debashish Bhattacharya [aut], Mark Ragan [aut], Cheong Xin Chan [aut, cph] (Original Perl implementation) |
| Maintainer: | Timothy Stephens <[email protected]> |
| License: | GPL (>= 3) |
| Version: | 1.0.9 |
| Built: | 2025-02-13 02:06:23 UTC |
| Source: | https://github.com/cran/PhySortR |
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).
| Package: | PhySortR |
| Type: | Package |
| Version: | 1.0.8 |
| Date: | 2018-07-20 |
| License: | GPL (>= 3) |
Timothy G. Stephens, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
Maintainer: Timothy G. Stephens <[email protected]>
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
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.
convert.eNewick(eNewick)convert.eNewick(eNewick)
eNewick |
phylogenetic tree in extended Newick format. |
phylogenetic tree in traditional Newick format.
### 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### 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
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.
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 )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 )
target.groups |
a set of one or more terms that represent the target leaves whose membership will
be tested in each clade during sorting. Multiple terms are to be separated by a comma
( |
min.support |
the minimum support (i.e. between 0-1 or 0-100) of a clade (Default = 0). Support
values missing from phylogenetic trees are interpreted as zero. A vector of values
can be provided if multiple support values (e.g., aLRT, UFboot) are present in the
tree (i.e., |
min.prop.target |
the minimum proportion (between 0.0-1.0) of target leaves to be present in a clade out of the total target leaves in the tree (Default = 0.7). |
in.dir |
directory containing the phylogenetic trees to be sorted (Default = current working directory). |
out.dir |
directory to be created within |
mode |
option to |
clades.sorted |
option to control if the function will sort for Exclusive ( |
extension |
the file extension of the tree files to be analyzed (Default = |
clade.exclusivity |
the minimum proportion (0.0 <= x < 1.0) of target leaves to interrupting leaves allowed in each non-exclusive clade (Default = 0.9). |
Will always return a list containing the names of the trees identified during sorting,
irrespective of the mode argument.
### 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$"))### 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$"))