R/print-methods.R

In phylobase: Base package for phylogenetic structures and comparative data

##' print a phylogeny
##' 
##' Prints a phylo4 or phylo4d object in data.frame format with user-friendly
##' column names
##' 
##' This is a user-friendly version of the tree representation, useful for
##' checking that objects were read in completely and translated correctly. The
##' phylogenetic tree is represented as a list of numbered nodes, linked in a
##' particular way through time (or rates of evolutionary change).  The topology
##' is given by the pattern of links from each node to its ancestor. Also given
##' are the taxon names, node type (root/internal/tip) and phenotypic data (if
##' any) associated with the node, and the branch length from the node to its
##' ancestor. A list of nodes (descendants) and ancestors is minimally required
##' for a phylo4 object.
##' 
##' @param x a \code{phylo4} tree or \code{phylo4d} tree+data object
##' @param edgeOrder in the data frame returned, the option 'pretty' returns the
##' internal nodes followed by the tips, the option 'real' returns the nodes in
##' the order they are stored in the edge matrix.
##' @param printall default prints entire tree. printall=FALSE returns the first
##' 6 rows
##' @return A data.frame with a row for each node (descendant), sorted as
##' follows: root first, then other internal nodes, and finally tips.\cr The
##' returned data.frame has the following columns:\cr \item{label}{Label for the
##' taxon at the node (usually species name).} \item{node}{Node number, i.e. the
##' number identifying the node in edge matrix.} \item{ancestor}{Node number
##' of the node's ancestor.} \item{branch.length}{The branch length connecting
##' the node to its ancestor (NAs if missing).} \item{node.type}{"root",
##' "internal", or "tip". (internally generated)} \item{data}{phenotypic data
##' associated with the nodes, with separate columns for each variable.}
##' @note This is the default show() method for phylo4, phylo4d. It prints the
##' user-supplied information for building a phylo4 object. For a full
##' description of the phylo4 S4 object and slots, see \code{\link{phylo4}}.
##' @author Marguerite Butler, Thibaut Jombart \email{jombart@@biomserv.univ-lyon1.fr}, Steve Kembel
##' @include setAs-methods.R
##' @keywords methods
##' @examples
##' 
##' 
##' tree.phylo <- ape::read.tree(text="((a,b),c);")
##' tree <- as(tree.phylo, "phylo4")
##' ##plot(tree,show.node=TRUE) ## plotting broken with empty node labels: FIXME
##' tip.data <- data.frame(size=c(1,2,3), row.names=c("a", "b", "c"))
##' treedata <- phylo4d(tree, tip.data)
##' plot(treedata)
##' print(treedata)
##' 
##' 
##' @aliases print
##' @rdname print-methods
setGeneric("print")

##' @rdname print-methods
##' @aliases print,phylo4-method
##' @exportMethod print
setMethod("print", signature(x="phylo4"),
   function(x, edgeOrder=c("pretty", "real"),
            printall=TRUE) {
       if(!nrow(edges(x))) {
           msg <- paste("Empty \'", class(x), "\' object\n", sep="")
           cat(msg)
       }
       else {
           toRet <- .phylo4ToDataFrame(x, edgeOrder)
           if (printall) {
               print(toRet)
           }
           else {
               print(head(toRet))
           }
       }
})

##' @rdname print-methods
##' @aliases show
##' @exportMethod show
setGeneric("show")

##' @rdname print-methods
##' @aliases show,phylo4-method
setMethod("show", signature(object="phylo4"),
   function(object) print(object))

##' @rdname print-methods
##' @aliases names
##' @exportMethod names
setGeneric("names")

##' @rdname print-methods
##' @aliases names,phylo4-method
setMethod("names", signature(x="phylo4"),
 function(x) {
    temp <- rev(names(attributes(x)))[-1]
    return(rev(temp))
})

##' @rdname print-methods
##' @aliases head
##' @exportMethod head
setGeneric("head")

##' @rdname print-methods
##' @aliases head,phylo4-method
setMethod("head", signature(x="phylo4"),
  function(x, n=20) {
      head(as(x,"data.frame"),n=n)
  })

##' @rdname print-methods
##' @aliases tail
##' @exportMethod tail
setGeneric("tail")

##' @rdname print-methods
##' @aliases tail,phylo4-method
setMethod("tail", signature(x="phylo4"),
  function(x, n=20) {
      tail(as(x, "data.frame"), n=n)
  })