Package treeio. January 1, 2019

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1 Package treeio January 1, 2019 Title Base Classes and Functions for Phylogenetic Tree Input and Output Version Base classes and functions for parsing and exporting phylogenetic trees. 'treeio' supports parsing analysis findings from commonly used software packages, allows linking external data to phylogeny and merging tree data obtained from different sources. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree. Depends R (>= 3.4.0) Imports ape, dplyr, jsonlite, magrittr, methods, rlang, rvcheck, tibble, tidytree, utils Suggests ggplot2, ggtree, knitr, prettydoc, testthat, tidyr VignetteBuilder knitr ByteCompile true License Artistic-2.0 URL BugReports LazyData true biocviews Software, Annotation, Clustering, DataImport, DataRepresentation, Alignment, MultipleSequenceAlignment RoxygenNote git_url git_branch master git_last_commit 07230cb git_last_commit_date Date/Publication Author Guangchuang Yu [aut, cre] (< Tommy Tsan-Yuk Lam [ctb, ths], Casey Dunn [ctb], Bradley Jones [ctb], Tyler Bradley [ctb] Maintainer Guangchuang Yu <guangchuangyu@gmail.com> 1

2 2 R topics documented: R topics documented: as.treedata.phylo drop.tip get.placements get.tree get.treetext getnodenum is.ggtree jplace-class label_branch_paml mask merge_tree Nnode.treedata phypml print.beastlist raxml2nwk read.astral read.beast read.codeml read.codeml_mlc read.fasta read.hyphy read.hyphy.seq read.iqtree read.jplace read.jtree read.newick read.nhx read.paml_rst read.phylip read.phylip.seq read.phylip.tree read.phylot read.r8s read.raxml rename_taxa root.phylo taxa_rename tree_subset write.beast write.jplace write.jtree Index 26

3 as.treedata.phylo 3 as.treedata.phylo as.treedata convert phylo to treedata ## S3 method for class 'phylo' as.treedata(tree, boot = NULL,...) tree boot Details input tree, a phylo object optional, can be bootstrap value from ape::boot.phylo... additional parameters converting phylo object to treedata object drop.tip drop.tip method drop.tip method drop.tip method drop.tip(object, tip,...) drop.tip(object, tip,...) ## S4 method for signature 'phylo' drop.tip(object, tip,...) object tip A treedata or phylo object a vector of mode numeric or character specifying the tips to delete... additional parameters

4 4 get.placements updated object Casey Dunn and Guangchuang Yu Source drop.tip for phylo object is a wrapper method of ape::drop.tip from the ape package. The documentation you should read for the drop.tip function can be found here: drop.tip See Also drop.tip nhx <- system.("extdata/nhx", "ADH.nhx", package="treeio") nhx <- read.nhx(nhx) drop.tip(nhx, c("adh2", "ADH1")) get.placements get.placements access placement information get.placements(tree,...) ## S3 method for class 'jplace' get.placements(tree, by = "best",...) tree tree object... additional parameters by one of best and all placement tibble

5 get.tree 5 get.tree get.tree access phylo slot get.tree(x,...) x tree object... additional parameters phylo object get.treetext get.treetext method access tree text (newick text) from tree object get.treetext(object,...) ## S4 method for signature 'treedata' get.treetext(object) object treedata object... additional parameter phylo object

6 6 is.ggtree getnodenum getnodenum calculate total number of nodes getnodenum(tree) Nnode2(tree) tree tree object number Guangchuang Yu getnodenum(rtree(30)) Nnode2(rtree(30)) is.ggtree is.ggtree test whether input object is produced by ggtree function is.ggtree(x) x object TRUE or FALSE

7 jplace-class 7 jplace-class Class "jplace" This class stores phylogenetic placements Class "jplace" This class stores phylogenetic placements Slots phylo phylo object for tree structure treetext newick tree string data associated data extrainfo extra information, reserve for merge_tree tree placements reserve for jplace to store placement information info extra information, e.g. metadata, software version etc. label_branch_paml label_branch_paml label branch for PAML to infer selection pressure using branch model label_branch_paml(tree, node, label) tree phylo object node node number label label of branch, e.g. #1 updated phylo object

8 8 merge_tree mask mask site mask mask(tree_object, field, site, mask_site = FALSE) tree_object field site mask_site tree object selected field site if TRUE, site will be masked. if FALSE, selected site will not be masked, while other sites will be masked. updated tree object Guangchuang Yu merge_tree merge_tree merge two tree object merge_tree(obj1, obj2) obj1 tree object 1 obj2 tree object 2 tree object Guangchuang Yu

9 Nnode.treedata 9 Nnode.treedata Nnode number of nodes ## S3 method for class 'treedata' Nnode(phy, internal.only = TRUE,...) phy internal.only treedata object whether only count internal nodes... additional parameters number of nodes Nnode(rtree(30)) phypml treeanno.pml tree annotation of sequence substitution by comparing to parent node phypml(pmltree, type = "ml") pmltree type tree in pml object, output of phangorn::optim.pml one of ml and bayes for inferring ancestral sequences phangorn object

10 10 raxml2nwk Yu Guangchuang print.beastlist print print information of a list of beast trees ## S3 method for class 'beastlist' print(x,...) x... no used message a list of beast object raxml2nwk raxml2nwk convert raxml bootstrap tree to newick format raxml2nwk(in, out = "raxml.tree") in out input output newick Guangchuang Yu

11 read.astral 11 read.astral read.astral parse ASTRAL output newick text read.astral() ASTRAL Newick treedata object Guangchuang Yu tt <- "((species1,(species2,species3)'[pp1=0.75;pp2=0.24;pp3=0.01]': )'[pp1=0.98;pp2=0.02;p read.astral(textconnection(tt)) read.beast read.beast read beast output read.beast() read.mrbayes() beast beast object Guangchuang Yu

12 12 read.codeml_mlc <- system.("extdata/beast", "beast_mcc.tree", package="treeio") read.beast() read.codeml read.codeml read baseml output read.codeml(rst, mlc, tree = "mlc", type = "Joint") rst mlc tree type rst mlc one of mlc or rst one of Marginal or Joint A treedata object Guangchuang Yu rst <- system.("extdata/paml_codeml", "rst", package="treeio") mlc <- system.("extdata/paml_codeml", "mlc", package="treeio") read.codeml(rst, mlc) read.codeml_mlc read.codeml_mlc read mlc of codeml output read.codeml_mlc(mlc) mlc mlc

13 read.fasta 13 A codeml_mlc object ygc mlc <- system.("extdata/paml_codeml", "mlc", package="treeio") read.codeml_mlc(mlc) read.fasta read.fasta read FASTA read.fasta(fasta) fasta fasta Details This function supports both DNA or AA sequences DNAbin or AAbin object

14 14 read.hyphy.seq read.hyphy read.hyphy read HYPHY output read.hyphy(nwk, ancseq, tip.fas = NULL) nwk ancseq tip.fas tree in nwk format, one of hyphy output ancestral sequence in nexus format, one of hyphy output tip sequence A hyphy object Guangchuang Yu nwk <- system.("extdata/hyphy", "labelledtree.tree", package="treeio") ancseq <- system.("extdata/hyphy", "ancseq.nex", package="treeio") read.hyphy(nwk, ancseq) read.hyphy.seq read.hyphy.seq parse sequences from hyphy output read.hyphy.seq() output of hyphy ancestral sequence inference; nexus format DNAbin object

15 read.iqtree 15 ancseq <- system.("extdata/hyphy", "ancseq.nex", package="treeio") read.hyphy.seq(ancseq) read.iqtree read.iqtree parse IQ-TREE output read.iqtree() IQ-TREE Newick text treedata object Guangchuang Yu read.jplace read.jplace read jplace read.jplace() jplace jplace instance

16 16 read.newick Guangchuang Yu jp <- system.("extdata", "sample.jplace", package="treeio") read.jplace(jp) read.jtree read.jtree Import tree data from jtree, which is JSON-based text and probably output by write.jtree read.jtree() tree treedata object read.newick read.newick read newick tree read.newick(, node.label = "label",...) newick node.label parse node label as label or support value... additional parameter, passed to read.tree

17 read.nhx 17 phylo or treedata object read.nhx read.nhx read nhx tree read.nhx() nhx nhx object Guangchuang Yu nhx <- system.("extdata/nhx", "ADH.nhx", package="treeio") read.nhx(nhx) read.paml_rst read.paml_rst read rst from paml (both baseml and codeml) output read.paml_rst(rst, type = "Joint") rst type rst one of Marginal or Joint

18 18 read.phylip A treedata object Guangchuang Yu rst <- system.("extdata/paml_baseml", "rst", package="treeio") read.paml_rst(rst) read.phylip read.phylip parsing phylip tree format read.phylip() phylip an instance of phylip Guangchuang Yu phy <- system.("extdata", "sample.phy", package="treeio") read.phylip(phy)

19 read.phylip.seq 19 read.phylip.seq read.phylip.seq read aligned sequences from phylip format read.phylip.seq() phylip, currently only sequential format is supported DNAbin object References read.phylip.tree read.phylip.tree parse tree from phylip read.phylip.tree() phylip phylo or multiphylo object

20 20 read.r8s read.phylot read.phylot parse output from phylot read.phylot(,...) newick tree... additional parameters to read.tree phylo object References read.r8s read.r8s parse output from r8s read.r8s() r8s output log multiphylo object Guangchuang Yu

21 read.raxml 21 read.r8s(system.("extdata/r8s", "H3_r8s_output.log", package="treeio")) read.raxml read.raxml parse RAxML bootstrapping analysis output read.raxml() RAxML bootstrapping analysis output treedata object Guangchuang Yu raxml_ <- system.("extdata/raxml", "RAxML_bipartitionsBranchLabels.H3", package="treeio") read.raxml(raxml_) rename_taxa rename_taxa rename tip label of phylogenetic tree rename_taxa(tree, data, key, value) tree data key value tree object, either treedata or phylo data frame column in data that match tip label column in data for rename tip label

22 22 taxa_rename tree object Guangchuang Yu root.phylo root re-root a tree ## S3 method for class 'phylo' root(object, node,...) ## S3 method for class 'treedata' root(object, node,...) object tree object node node to reroot... additional parameters rerooted tree Guangchuang Yu taxa_rename taxa_rename rename taxa taxa_rename(tree, name)

23 tree_subset 23 tree name tree object a two column data.frame contains original name in 1st column and new name in 2nd column updated tree object with new taxa name tree_subset Subset tree objects by related nodes This function allows for a tree object to be subset by specifying a node and returns all related nodes within a selected number of levels tree_subset(tree, node, levels_back = 5, group_node = TRUE) ## S3 method for class 'phylo' tree_subset(tree, node, levels_back = 5, group_node = TRUE) ## S3 method for class 'treedata' tree_subset(tree, node, levels_back = 5, group_node = TRUE) tree node levels_back group_node a tree object of class phylo either a tip label or a node number for the given tree that will be the focus of the subsetted tree a number specifying how many nodes back from the selected node the subsetted tree should include whether add grouping information of selected node Details This function will take a tree and a specified node from that tree and subset the tree showing all relatives back to a specified number of nodes. This function allows for a combination of ancestor and offspring to return a subsetted tree that is of class phylo. This allows for easy graphing of the tree with ggtree

24 24 write.beast ## Not run: nwk <- system.("extdata", "sample.nwk", package="treeio") tree <- read.tree(nwk) sub_tree <- tree_subset(tree, node = "A", levels_back = 3) ggtree(sub_tree) + geom_tiplab() + geom_nodelab() ## End(Not run) ## Not run: nwk <- system.("extdata", "sample.nwk", package="treeio") tree <- read.tree(nwk) sub_tree <- tree_subset(tree, node = "A", levels_back = 3) ggtree(sub_tree) + geom_tiplab() + geom_nodelab() ## End(Not run) write.beast write.beast Export treedata object to BEAST NEXUS. This function was adopted and modified from ape::write.nexus write.beast(treedata, = "", translate = TRUE, tree.name = "UNTITLED") treedata translate tree.name treedata object output. If = "", print the output content on screen whether translate taxa labels name of the tree output or content on screen nhx <- system.("extdata/nhx", "phyldog.nhx", package="treeio") nhx <- read.nhx(nhx) write.beast(nhx)

25 write.jplace 25 write.jplace write.jplace generate jplace write.jplace(nwk, data, out) nwk data out tree in newick format annotation data jplace output jplace ygc write.jtree write.jtree Export treedata object to json tree write.jtree(treedata, = "") treedata treedata object output. If = "", print the output content on screen output or content on screen

26 Index Topic classes jplace-class, 7 as.treedata.phylo, 3 drop.tip, 3, 4 drop.tip,phylo (drop.tip), 3 drop.tip,phylo-method (drop.tip), 3 drop.tip,treedata (drop.tip), 3 drop.tip,treedata-method (drop.tip), 3 get.placements, 4 get.tree, 5 get.treetext, 5 get.treetext,treedata-method (get.treetext), 5 getnodenum, 6 is.ggtree, 6 read.newick, 16 read.nhx, 17 read.paml_rst, 17 read.phylip, 18 read.phylip.seq, 19 read.phylip.tree, 19 read.phylot, 20 read.r8s, 20 read.raxml, 21 rename_taxa, 21 root.phylo, 22 root.treedata (root.phylo), 22 taxa_rename, 22 tree_subset, 23 write.beast, 24 write.jplace, 25 write.jtree, 25 jplace-class, 7 label_branch_paml, 7 mask, 8 merge_tree, 8 Nnode.treedata, 9 Nnode2 (getnodenum), 6 phypml, 9 print.beastlist, 10 raxml2nwk, 10 read.astral, 11 read.beast, 11 read.codeml, 12 read.codeml_mlc, 12 read.fasta, 13 read.hyphy, 14 read.hyphy.seq, 14 read.iqtree, 15 read.jplace, 15 read.jtree, 16 read.mrbayes (read.beast), 11 26