@@ -1,20 +1,35 @@

 Package: ggtree

 Type: Package

-Title: a phylogenetic tree viewer for different types of tree

-        annotations

-Version: 0.99.5

+Title: a phylogenetic tree viewer for different types of tree annotations

+Version: 0.99.6

 Author: Guangchuang Yu

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

-Description: ggtree extends the ggplot2 plotting system which

-        implemented the grammar of graphics. ggtree is designed for

-        visualizing phylogenetic tree and different types of associated

-        annotation data.

-Depends: R (>= 3.1.0), ape, ggplot2

-Imports: Biostrings, grid, gridExtra, jsonlite, magrittr, methods,

-        reshape2, stats4

-Suggests: phylobase, BiocStyle, knitr, testthat, rmarkdown

+Description: ggtree extends the ggplot2 plotting system which implemented the

+    grammar of graphics. ggtree is designed for visualizing phylogenetic tree

+    and different types of associated annotation data.

+Depends:

+    R (>= 3.1.0)

+Imports:

+    ape,

+    Biostrings,

+    ggplot2,

+    grid,

+    gridExtra,

+    jsonlite,

+    magrittr,

+    methods,

+    reshape2,

+    stats4

+Suggests:

+    phylobase,

+    BiocStyle,

+    colorspace,

+    knitr,

+    testthat,

+    rmarkdown

 VignetteBuilder: knitr

 License: Artistic-2.0

 URL: https://github.com/GuangchuangYu/ggtree

 BugReports: https://github.com/GuangchuangYu/ggtree/issues

+Packaged: 2014-12-03 08:16:14 UTC; root

 biocViews: Visualization

@@ -13,19 +13,26 @@ S3method(fortify,phylo4)

 export("%<%")

 export("%<+%")

 export(.)

+export(aes)

 export(as.binary)

 export(geom_aline)

+export(geom_text)

 export(geom_tiplab)

 export(geom_tippoint)

 export(geom_tree)

 export(get.fields)

+export(get.offspring.tip)

 export(get.placements)

 export(get.subs)

+export(get.tipseq)

 export(get.tree)

 export(get.treeinfo)

 export(get.treetext)

+export(ggplotGrob)

 export(ggtree)

 export(gplot)

+export(groupOTU)

+export(gzoom)

 export(plot)

 export(read.baseml)

 export(read.beast)

@@ -34,6 +41,8 @@ export(read.codeml_mlc)

 export(read.hyphy)

 export(read.jplace)

 export(read.paml_rst)

+export(read.tree)

+export(rtree)

 export(theme_tree)

 export(theme_tree2)

 export(write.jplace)

@@ -46,15 +55,18 @@ exportClasses(paml_rst)

 exportMethods(get.fields)

 exportMethods(get.placements)

 exportMethods(get.subs)

+exportMethods(get.tipseq)

 exportMethods(get.tree)

 exportMethods(get.treeinfo)

 exportMethods(get.treetext)

+exportMethods(groupOTU)

 exportMethods(plot)

 exportMethods(show)

 importFrom(Biostrings,GENETIC_CODE)

 importFrom(Biostrings,readBStringSet)

 importFrom(Biostrings,toString)

 importFrom(ape,Ntip)

+importFrom(ape,drop.tip)

 importFrom(ape,extract.clade)

 importFrom(ape,is.binary.tree)

 importFrom(ape,ladderize)

@@ -62,6 +74,7 @@ importFrom(ape,print.phylo)

 importFrom(ape,read.nexus)

 importFrom(ape,read.tree)

 importFrom(ape,reorder.phylo)

+importFrom(ape,which.edge)

 importFrom(ape,write.tree)

 importFrom(ggplot2,"%+replace%")

 importFrom(ggplot2,aes)

@@ -79,11 +92,13 @@ importFrom(ggplot2,geom_segment)

 importFrom(ggplot2,geom_text)

 importFrom(ggplot2,geom_tile)

 importFrom(ggplot2,ggplot)

+importFrom(ggplot2,scale_color_manual)

 importFrom(ggplot2,scale_fill_gradient)

 importFrom(ggplot2,scale_x_reverse)

 importFrom(ggplot2,theme)

 importFrom(ggplot2,theme_bw)

 importFrom(ggplot2,xlab)

+importFrom(ggplot2,xlim)

 importFrom(ggplot2,ylab)

 importFrom(grid,unit)

 importFrom(gridExtra,grid.arrange)

@@ -1,5 +1,14 @@

+CHANGES IN VERSION 0.99.6

+------------------------

+ o add example of gzoom and groupOTU in vignette <2015-01-14, Wed> 

+ o implement groupOTU methods <2015-01-14, Wed>

+ o export get.offspring.tip <2015-01-14, Wed>

+

 CHANGES IN VERSION 0.99.5

 ------------------------

+ o move ape and ggplot2 from Depends to Imports <2015-01-12, Mon>

+ o get.tipseq method for paml_rst and codeml object <2015-01-08, Thu>

+ o add gzoom function, similar to zoom function in ape <2015-01-07, Wed>

  o add examples in man pages of %<% and %<+% operators <2015-01-06, Tue>

  o remove <<- and update vignette <2015-01-06, Tue>

  o update vignette and use BibTex and CSL for references <2015-01-05, Mon>  

@@ -146,6 +146,7 @@ setClass("codeml",

 ##' @docType class

 ##' @slot fields colnames of first variable of placements

 ##' @slot treetext tree text

+##' @slot phylo tree phylo object

 ##' @slot placements placement information

 ##' @slot version version

 ##' @slot metadata metadata

@@ -159,6 +160,7 @@ setClass("jplace",

          representation = representation(

              fields     = "character",

              treetext   = "character",

+             phylo      = "phylo",

              placements = "data.frame",

              version    = "numeric",

              metadata   = "list",

@@ -93,3 +93,24 @@ setGeneric("get.placements", function(object, by, ...) standardGeneric("get.plac

 setGeneric("get.subs", function(object, type, ...) standardGeneric("get.subs"))

+##' @docType methods

+##' @name get.tipseq

+##' @rdname get.tipseq-methods

+##' @title get.tipseq method

+##' @param object one of paml_rst or codeml object

+##' @param ... additional parameter

+##' @return character

+##' @export

+setGeneric("get.tipseq", function(object, ...) standardGeneric("get.tipseq"))

+

+##' @docType methods

+##' @name groupOTU

+##' @rdname groupOTU-methods

+##' @title groupOTU method

+##' @param object supported objects, including phylo, paml_rst,

+##'               codeml_mlc, codeml, jplace, beast, hyphy

+##' @param focus a vector of tip (label or number) or a list of tips.

+##' @return group index

+##' @export

+setGeneric("groupOTU", function(object, focus) standardGeneric("groupOTU"))

+

new file mode 100644

@@ -0,0 +1,45 @@

+##' read newick tree

+##' @export

+##' @rdname read.tree

+##' @param file file name

+##' @param text alternatively, using newick text

+##' @param tree.names if read several trees, specify their names

+##' @param skip number of lines of the input file to skip

+##' @param comment.char a single character,

+##'                     the remaining of the line after this character is ignored.

+##' @param keep.multi if 'TRUE' and 'tree.names = NULL'

+##'                   then single trees are returned in 'multiPhylo' format

+##'                   with any name that is present. Default is 'FALSE'

+##' @param ... further arguments to be passed to 'scan()'.

+##' @source

+##' This is just the imported function

+##' from the ape package. The documentation you should

+##' read for the read.tree function can be found here: \link[ape]{read.tree}

+##'

+##' @seealso

+##' \link[ape]{read.tree}

+read.tree <- ape::read.tree

+

+

+##' generate random tree

+##' @export

+##' @rdname rtree

+##' @param n number of tips in the tree

+##' @param rooted logcial

+##' @param tip.label tip label

+##' @param br one of the following: (i) an R function used to generate the

+##'           branch lengths ('rtree'; use 'NULL' to simulate only a

+##'           topology), or the coalescence times ('rcoal'); (ii) a

+##'           character to simulate a genuine coalescent tree for 'rcoal'

+##'           (the default); or (iii) a numeric vector for the branch

+##'           lengths or the coalescence times.

+##' @param ... additional parameters to be passed to 'br'

+##' @source

+##' This is just the imported function

+##' from the ape package. The documentation you should

+##' read for the rtree function can be found here: \link[ape]{rtree}

+##'

+##' @seealso

+##' \link[ape]{rtree}

+rtree <- ape::rtree

+

@@ -81,6 +81,13 @@ setMethod("show", signature(object = "beast"),

               print_fields(object)              

           })

+##' @rdname groupOTU-methods

+##' @exportMethod groupOTU

+setMethod("groupOTU", signature(object="beast"),

+          function(object, focus) {

+              groupOTU_(object, focus)

+          }

+          )

 ##' get.tree method

 ##'

@@ -22,6 +22,14 @@ read.codeml <- function(rstfile, mlcfile) {

 }

+##' @rdname groupOTU-methods

+##' @exportMethod groupOTU

+setMethod("groupOTU", signature(object="codeml"),

+          function(object, focus) {

+              groupOTU_(object, focus)

+          }

+          )

+

 ##' @rdname show-methods

 ##' @exportMethod show

 setMethod("show", signature(object = "codeml"),

@@ -36,6 +44,12 @@ setMethod("show", signature(object = "codeml"),

               print_fields(object, len=4)

           })

+##' @rdname get.tipseq-methods

+##' @exportMethod get.tipseq

+setMethod("get.tipseq", signature(object = "codeml"),

+          function(object, ...) {

+              return(object@rst@tip_seq)

+          })

 ##' @rdname get.tree-methods

 ##' @exportMethod get.tree

@@ -78,7 +92,7 @@ setMethod("plot", signature(x = "codeml"),

                    tip.label.size   = 4,

                    tip.label.hjust  = -0.1,

                    position         = "branch",

-                   annotation       = "dN.dS",

+                   annotation       = "dN_vs_dS",

                    annotation.size  = 3,

                    annotation.color = "black",

                    ndigits          = 2,

@@ -23,6 +23,14 @@ read.codeml_mlc <- function(mlcfile) {

         mlcfile  = mlcfile)

 }

+##' @rdname groupOTU-methods

+##' @exportMethod groupOTU

+setMethod("groupOTU", signature(object="codeml_mlc"),

+          function(object, focus) {

+              groupOTU_(object, focus)

+          }

+          )

+

 ##' @rdname show-methods

 ##' @exportMethod show

 setMethod("show", signature(object = "codeml_mlc"),

new file mode 100644

@@ -0,0 +1,47 @@

+##' creates a lists of unevaluated expressions

+##' @export

+##' @rdname aes

+##' @param x name values

+##' @param y name values

+##' @param ... additional name values

+##' @source

+##' This is just the imported function

+##' from the ggplot2 package. The documentation you should

+##' read for the aes function can be found here: \link[ggplot2]{aes}

+##'

+##' @seealso

+##' \link[ggplot2]{aes}

+aes <- ggplot2::aes

+

+

+##' generate a ggplot2 plot grob

+##' @export

+##' @rdname ggplotGrob

+##' @param x ggplot2 object

+##' @source

+##' This is just the imported function

+##' from the ggplot2 package. The documentation you should

+##' read for the ggplotGrob function can be found here: \link[ggplot2]{ggplotGrob}

+##' 

+##' @seealso

+##' \link[ggplot2]{ggplotGrob}

+ggplotGrob <- ggplot2::ggplotGrob

+

+##' text annotations

+##' @export

+##' @rdname geom_text

+##' @param mapping the aesthetic mapping

+##' @param data A layer specific dataset -

+##'             only needed if you want to override he plot defaults.

+##' @param stat The statistical transformation to use on the data for this layer

+##' @param position The position adjustment to use for overlapping points on this layer

+##' @param parse if TRUE, the labels will be passd into expressions

+##' @param ... other arguments passed on to 'layer'

+##' @source

+##' This is just the imported function

+##' from the ggplot2 package. The documentation you should

+##' read for the geom_text function can be found here: \link[ggplot2]{geom_text}

+##'

+##' @seealso

+##' \link[ggplot2]{geom_text}

+geom_text <- ggplot2::geom_text

@@ -89,6 +89,14 @@ setMethod("plot", signature(x = "hyphy"),

                         annotation.size,...)

           })

+##' @rdname groupOTU-methods

+##' @exportMethod groupOTU

+setMethod("groupOTU", signature(object="hyphy"),

+          function(object, focus) {

+              groupOTU_(object, focus)

+          }

+          )

+

 ##' @rdname show-methods

 ##' @exportMethod show

 setMethod("show", signature(object = "hyphy"),

@@ -17,6 +17,7 @@ read.jplace <- function(file) {

          new("jplace",

              fields     = fields,

              treetext   = tree,

+             phylo      = jplace_treetext_to_phylo(tree),

              placements = placements,

              version    = version,

              metadata   = metadata,

@@ -25,12 +26,19 @@ read.jplace <- function(file) {

          )

 }

+##' @rdname groupOTU-methods

+##' @exportMethod groupOTU

+setMethod("groupOTU", signature(object="jplace"),

+          function(object, focus) {

+              groupOTU_(object, focus)

+          }

+          )

 ##' @rdname get.tree-methods

 ##' @exportMethod get.tree

 setMethod("get.tree", signature(object="jplace"),

           function(object) {

-              jplace_treetext_to_phylo(object@treetext)

+              object@phylo

           })

@@ -138,7 +146,6 @@ setMethod("get.fields", signature(object = "jplace"),

           }

           )

-

 ##' get.placement method

 ##'

 ##'

@@ -200,8 +207,7 @@ get.fields.jplace <- function(object, ...) {

 get.treeinfo.jplace <- function(object, layout,

                                 ladderize, right, ...) {

-    tree.text <- get.treetext(object)

-    extract.treeinfo.jplace(tree.text, layout,

+    extract.treeinfo.jplace(object, layout,

                             ladderize, right)

 }

@@ -17,9 +17,7 @@ read.tip_seq_mlc <- function(mlcfile) {

     return(res)

 }

-read.tip_seq_mlb <- function(mlbfile) {

-    read.tip_seq_mlc(mlbfile)

-}

+read.tip_seq_mlb <- read.tip_seq_mlc

 read.dnds_mlc <- function(mlcfile) {

     mlc <- readLines(mlcfile)

@@ -114,7 +112,7 @@ read.phylo_paml_mlc <- function(mlcfile) {

                     jj <- which(treeinfo.tr3[, "node"] == jp)

                     treeinfo[ii, "label"] <- as.character(ip)

                     treeinfo.tr3[jj, "label"] <- as.character(ip)

-                    treeinfo[ii, "length"] <- treeinfo.tr3[jj, "length"]

+                    treeinfo[ii, "length"] <- treeinfo.tr3[jj, "branch.length"]

                     pNode <- c(pNode, ip)

                 }

                 treeinfo[ii, "visited"] <- TRUE

@@ -60,6 +60,25 @@ read.paml_rst <- function(rstfile, tip.fasfile = NULL) {

     set.paml_rst_(res)

 }

+##' @rdname groupOTU-methods

+##' @exportMethod groupOTU

+setMethod("groupOTU", signature(object="paml_rst"),

+          function(object, focus) {

+              groupOTU_(object, focus)

+          }

+          )

+

+

+##' @rdname get.tipseq-methods

+##' @exportMethod get.tipseq

+setMethod("get.tipseq", signature(object="paml_rst"),

+          function(object, ...) {

+              if (length(object@tip_seq) == 0) {

+                  warning("tip sequence not available...\n")

+              } else {

+                  object@tip_seq

+              }

+          })

 ##' @rdname show-methods

 ##' @exportMethod show

@@ -1,3 +1,100 @@

+##' @rdname groupOTU-methods

+##' @exportMethod groupOTU

+setMethod("groupOTU", signature(object="phylo"),

+          function(object, focus) {

+              groupOTU.phylo(object, focus)

+          })

+

+

+groupOTU_ <- function(object, focus) {

+    groupOTU.phylo(get.tree(object), focus)

+}

+

+##' group OTU

+##'

+##' 

+##' @title groupOTU.phylo

+##' @param phy tree object

+##' @param focus tip list

+##' @return cluster index

+##' @author ygc

+groupOTU.phylo <- function(phy, focus) {

+    if ( is(focus, "list") ) {

+        for (i in 1:length(focus)) {

+            phy <- gfocus(phy, focus[[i]])

+        } 

+    } else {

+        phy <- gfocus(phy, focus)

+    }

+    attr(phy, "focus")

+}

+

+##' @importFrom ape which.edge

+gfocus <- function(phy, focus) {

+    if (is.character(focus)) {

+        focus <- which(phy$tip.label %in% focus)

+    }

+    

+    n <- getNodeNum(phy)

+    if (is.null(attr(phy, "focus"))) {

+        foc <- rep(1, 2*n)

+    } else {

+        foc <- attr(phy, "focus")

+    }

+    i <- max(foc) + 1

+    sn <- phy$edge[which.edge(phy, focus),] %>% as.vector %>% unique

+    foc[sn] <- i

+    foc[sn+n] <- i

+    attr(phy, "focus") <- foc

+

+    ## sn <- which(df$focus != 1)

+    ## df$focus[df$parent] -> f2

+    ## f2[-sn] <- 1

+

+    phy

+}

+

+##' plots simultaneously a whole phylogenetic tree and a portion of it. 

+##'

+##' 

+##' @title gzoom

+##' @param phy phylo object

+##' @param focus selected tips

+##' @param subtree logical

+##' @param widths widths

+##' @return a list of ggplot object

+##' @importFrom ggplot2 xlim

+##' @importFrom ggplot2 scale_color_manual

+##' @importFrom ape drop.tip

+##' @export

+##' @author ygc

+##' @examples

+##' require(ape)

+##' data(chiroptera)

+##' gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))

+gzoom <- function(phy, focus, subtree=FALSE, widths=c(.3, .7)) {

+    if (is.character(focus)) {

+        focus <- which(phy$tip.label %in% focus)

+    }

+

+    phy <- gfocus(phy, focus)

+

+    foc <- attr(phy, "focus")

+    cols <- c("black", "red")[foc]

+    

+    p1 <- ggplot(phy) + geom_tree(colour=cols) +

+        xlab("") + ylab("") + theme_tree()

+    

+    subtr <- drop.tip(phy, phy$tip.label[-focus],

+                      subtree=subtree, rooted=TRUE)

+    

+    p2 <- ggtree(subtr, color="red") + geom_tiplab(hjust=-0.05)

+    p2 <- p2 + xlim(0, max(p2$data$x)*1.2)

+    grid.arrange(p1, p2, ncol=2, widths=widths)

+    

+    invisible(list(p1=p1, p2=p2))

+}

+

 ##' update tree 

 ##'

@@ -10,6 +107,7 @@

 ##' @export

 ##' @author Yu Guangchuang

 ##' @examples

+##' library("ggplot2")

 ##' nwk <- system.file("extdata", "sample.nwk", package="ggtree")

 ##' tree <- read.tree(nwk)

 ##' p <- ggtree(tree) + geom_point(subset=.(!isTip), 

@@ -103,7 +201,16 @@ layout.unrooted <- function(tree) {

 }

+##' extract offspring tips

+##'

+##' 

+##' @title get.offspring.tip

+##' @param tr tree

+##' @param node node

+##' @return tip label

+##' @author ygc

 ##' @importFrom ape extract.clade

+##' @export

 get.offspring.tip <- function(tr, node) {

     if ( ! node %in% tr$edge[,1]) {

         ## return itself

@@ -337,7 +337,9 @@ fortify.phylo <- function(model, data, layout="phylogram",

     idx <- is.na(df$parent)

     df$parent[idx] <- df$node[idx]

     rownames(df) <- df$node

-    

+    cn <- colnames(df)

+    colnames(df)[grep("length", cn)] <- "branch.length"

+

     return(df)

 }

@@ -399,7 +401,9 @@ as.data.frame.phylo_ <- function(x, layout="phylogram",

     isTip[1:Ntip] <- TRUE

     res$isTip <- isTip

     res$branch <- (res$x[res$parent] + res$x)/2

-    res$length[is.na(res$length)] <- 0

+    if (!is.null(res$length)) {

+        res$length[is.na(res$length)] <- 0

+    }

     res$branch[is.na(res$branch)] <- 0

     return(res)

 }

@@ -149,26 +149,38 @@ reverse.treeview.data <- function(df) {

 jplace_treetext_to_phylo <- function(tree.text) {

     ## move edge label to node label separate by @

     tr <- gsub('(:[0-9.e-]+)\\{(\\d+)\\}', '\\@\\2\\1', tree.text)

-    read.tree(text=tr)

+    phylo <- read.tree(text=tr)

+    if (length(grep('@', phylo$tip.label)) > 0) {

+        phylo$node.label[1] %<>% gsub("(.*)\\{(\\d+)\\}", "\\1@\\2", .)

+        tip.edgeNum <- as.numeric(gsub("[^@]*@(\\d*)", "\\1",phylo$tip.label))

+        node.edgeNum <- as.numeric(gsub("[^@]*@(\\d*)", "\\1",phylo$node.label))

+        phylo$tip.label %<>% gsub("@\\d+", "", .)

+        phylo$node.label %<>% gsub("@\\d+", "", .)

+        if (all(phylo$node.label == "")) {

+            phylo$node.label <- NULL

+        }

+

+        N <- getNodeNum(phylo)

+        edgeNum.df <- data.frame(node=1:N, edgeNum=c(tip.edgeNum, node.edgeNum))

+        edgeNum.df <- edgeNum.df[!is.na(edgeNum.df[,2]),]

+        edgeNum <- edgeNum.df[match( phylo$edge[,2], edgeNum.df$node), 2]

+        attr(phylo, "edgeNum") <- edgeNum

+    }

+    return(phylo)

 }

-extract.treeinfo.jplace <- function(tree.text, layout="phylogram", ladderize=TRUE, right=FALSE) {

+extract.treeinfo.jplace <- function(object, layout="phylogram", ladderize=TRUE, right=FALSE) {

-    tree <- jplace_treetext_to_phylo(tree.text)

+    tree <- get.tree(object)

     df <- fortify.phylo(tree, layout=layout, ladderize=ladderize, right=right)

-    root.idx <- which(df$parent == df$node)

-    root.lab <- df[,"label"]

-    df$label[root.idx] <- gsub("(.*)\\{(\\d+)\\}", "\\1@\\2", df$label[root.idx])

-

-    if ( length(grep('@', df$label)) > 0) {

-        df$edge <- as.numeric(gsub("[^@]*@(\\d*)", "\\1",df$label))

+    edgeNum <- attr(tree, "edgeNum")

+    if (!is.null(edgeNum)) {

+        edgeNum.df <- data.frame(node=tree$edge[,2], edge=edgeNum)

+        df2 <- merge(df, edgeNum.df, by.x="node", by.y="node", all.x=TRUE) 

+        df <- df2[match(df[, "node"], df2[, "node"]),]

     }

-    

-    ## remove edge label from node label

-    df$label <- gsub("@\\d*", "", df$label)

-    df$label[df$label == ""] <- NA

     attr(df, "ladderize") <- ladderize

     attr(df, "right") <- right

     return(df)

new file mode 100644

@@ -0,0 +1,21 @@

+citHeader("To cite ggtree in publications use:")

+

+citEntry(

+    entry  = "article",

+    title  = "ggtree: a phylogenetic tree viewer for different types of tree annotations",

+    author = personList(

+        as.person("Guangchuang Yu")

+    ),

+    year    = "2015",

+    journal = "submitted",

+    volume  = "",

+    issue   = "",

+    number  = "",

+    pages   = "",

+    doi     = "",

+    PMID    = "",

+    url     = "", 

+    textVersion =

+        "Guangchuang Yu. (2015) ggtree: a phylogenetic tree viewer for different types of tree annotations. submitted"

+)

+

new file mode 100644

@@ -0,0 +1,27 @@

+% Generated by roxygen2 (4.1.0): do not edit by hand

+% Please edit documentation in R/ggplot2.R

+\name{aes}

+\alias{aes}

+\title{creates a lists of unevaluated expressions}

+\source{

+This is just the imported function

+from the ggplot2 package. The documentation you should

+read for the aes function can be found here: \link[ggplot2]{aes}

+}

+\usage{

+aes(x, y, ...)

+}

+\arguments{

+\item{x}{name values}

+

+\item{y}{name values}

+

+\item{...}{additional name values}

+}

+\description{

+creates a lists of unevaluated expressions

+}

+\seealso{

+\link[ggplot2]{aes}

+}

+

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+% Generated by roxygen2 (4.1.0): do not edit by hand

+% Please edit documentation in R/ggplot2.R

+\name{geom_text}

+\alias{geom_text}

+\title{text annotations}

+\source{

+This is just the imported function

+from the ggplot2 package. The documentation you should

+read for the geom_text function can be found here: \link[ggplot2]{geom_text}

+}

+\usage{

+geom_text(mapping = NULL, data = NULL, stat = "identity",

+  position = "identity", parse = FALSE, ...)

+}

+\arguments{

+\item{mapping}{the aesthetic mapping}

+

+\item{data}{A layer specific dataset -

+only needed if you want to override he plot defaults.}

+

+\item{stat}{The statistical transformation to use on the data for this layer}

+

+\item{position}{The position adjustment to use for overlapping points on this layer}

+

+\item{parse}{if TRUE, the labels will be passd into expressions}

+

+\item{...}{other arguments passed on to 'layer'}

+}

+\description{

+text annotations

+}

+\seealso{

+\link[ggplot2]{geom_text}

+}

+

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+% Generated by roxygen2 (4.1.0): do not edit by hand

+% Please edit documentation in R/tree.R

+\name{get.offspring.tip}

+\alias{get.offspring.tip}

+\title{get.offspring.tip}

+\usage{

+get.offspring.tip(tr, node)

+}

+\arguments{

+\item{tr}{tree}

+

+\item{node}{node}

+}

+\value{

+tip label

+}

+\description{

+extract offspring tips

+}

+\author{

+ygc

+}

+

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+% Generated by roxygen2 (4.1.0): do not edit by hand

+% Please edit documentation in R/AllGenerics.R, R/codeml.R, R/paml_rst.R

+\docType{methods}

+\name{get.tipseq}

+\alias{get.tipseq}

+\alias{get.tipseq,codeml-method}

+\alias{get.tipseq,paml_rst-method}

+\title{get.tipseq method}

+\usage{

+get.tipseq(object, ...)

+

+\S4method{get.tipseq}{codeml}(object, ...)

+

+\S4method{get.tipseq}{paml_rst}(object, ...)

+}

+\arguments{

+\item{object}{one of paml_rst or codeml object}

+

+\item{...}{additional parameter}

+}

+\value{

+character

+}

+\description{

+get.tipseq method

+}

+

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+% Generated by roxygen2 (4.1.0): do not edit by hand

+% Please edit documentation in R/ggplot2.R

+\name{ggplotGrob}

+\alias{ggplotGrob}

+\title{generate a ggplot2 plot grob}

+\source{

+This is just the imported function

+from the ggplot2 package. The documentation you should

+read for the ggplotGrob function can be found here: \link[ggplot2]{ggplotGrob}

+}

+\usage{

+ggplotGrob(x)

+}

+\arguments{

+\item{x}{ggplot2 object}

+}

+\description{

+generate a ggplot2 plot grob

+}

+\seealso{

+\link[ggplot2]{ggplotGrob}

+}

+

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+% Generated by roxygen2 (4.1.0): do not edit by hand

+% Please edit documentation in R/AllGenerics.R, R/beast.R, R/codeml.R, R/codeml_mlc.R, R/hyphy.R, R/jplace.R, R/paml_rst.R, R/tree.R

+\docType{methods}

+\name{groupOTU}

+\alias{groupOTU}

+\alias{groupOTU,beast-method}

+\alias{groupOTU,codeml-method}

+\alias{groupOTU,codeml_mlc-method}

+\alias{groupOTU,hyphy-method}

+\alias{groupOTU,jplace-method}

+\alias{groupOTU,paml_rst-method}

+\alias{groupOTU,phylo-method}

+\title{groupOTU method}

+\usage{

+groupOTU(object, focus)

+

+\S4method{groupOTU}{beast}(object, focus)

+

+\S4method{groupOTU}{codeml}(object, focus)

+

+\S4method{groupOTU}{codeml_mlc}(object, focus)

+

+\S4method{groupOTU}{hyphy}(object, focus)

+

+\S4method{groupOTU}{jplace}(object, focus)

+

+\S4method{groupOTU}{paml_rst}(object, focus)

+

+\S4method{groupOTU}{phylo}(object, focus)

+}

+\arguments{

+\item{object}{supported objects, including phylo, paml_rst,

+codeml_mlc, codeml, jplace, beast, hyphy}

+

+\item{focus}{a vector of tip (label or number) or a list of tips.}