1. ggtree
  2. R
  3. method-get-tree.R
Browse code

clean up code

guangchuang yu authored on 14/12/2017 08:47:21
Showing 1 changed files
R/method-get-tree.R
History View file @ 14ff9149
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deleted file mode 100644
... ... 
@@ -1,90 +0,0 @@
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-## ##' @rdname get.tree-methods
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-## ##' @exportMethod get.tree
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-## setMethod("get.tree", signature(object="apeBootstrap"),
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-##           function(object,...) {
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-##               object@phylo
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-##           }
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-##           )
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-
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-## ##' get.tree method
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-## ##'
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-## ##'
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-## ##' @docType methods
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-## ##' @name get.tree
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-## ##' @rdname get.tree-methods
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-## ##' @aliases get.tree,beast
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-## ##' @exportMethod get.tree
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-## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
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-## ##' @usage get.tree(object, ...)
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-## setMethod("get.tree", signature(object="beast"),
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-##           function(object,...) {
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-##               object@phylo
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-##           }
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-##           )
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-
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-
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-## ##' @rdname get.tree-methods
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-## ##' @exportMethod get.tree
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-## ##' @param by one of rst or mlc
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-## setMethod("get.tree", signature(object="codeml"),
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-##           function(object, by="rst", ...) {
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-##               if (by == "rst") {
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-##                   return(object@rst@phylo)
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-##               } else {
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-##                   return(object@mlc@phylo)
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-##               }
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-##           })
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-
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-
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-## ##' @rdname get.tree-methods
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-## ##' @exportMethod get.tree
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-## setMethod("get.tree", signature(object="jplace"),
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-##           function(object) {
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-##               object@phylo
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-##           })
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-
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-## ##' @rdname get.tree-methods
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-## ##' @exportMethod get.tree
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-## setMethod("get.tree", signature(object = "nhx"),
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-##           function(object) {
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-##               object@phylo
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-##           }
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-##           )
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-
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-## ##' @rdname get.tree-methods
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-## ##' @exportMethod get.tree
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-## setMethod("get.tree", signature(object="phylip"),
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-##           function(object,...) {
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-##               object@phylo
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-##           }
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-##           )
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-
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-## ##' @rdname get.tree-methods
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-## ##' @exportMethod get.tree
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-## setMethod("get.tree", signature(object="phylo"),
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-##           function(object, ...) {
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-##               return(object)
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-##           })
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-
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-## ##' @rdname get.tree-methods
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-## ##' @exportMethod get.tree
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-## setMethod("get.tree", signature(object="data.frame"),
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-##           function(object, ...) {
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-##               edge <- object[, c("parent", "node")]
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-##               i <- which(edge[,1] != 0 & edge[,1] != edge[,2])
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-##               edge <- edge[i, ]
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-##               edge.length <- object[i, "branch.length"]
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-##               tip.label <- object[object[, "isTip"], "label"]
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-##               phylo <- list(edge = as.matrix(edge),
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-##                   edge.length = edge.length,
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-##                   tip.label = tip.label)
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-
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-##               node.label <- object[!object[, "isTip"], "label"]
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-##               if (!all(is.na(node.label))) {
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-##                   phylo$node.label <- node.label
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-##               }
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-##               phylo$Nnode <- sum(!object[, "isTip"])
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-##               class(phylo) <- "phylo"
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-##               return(phylo)
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-##           })
90 
-
Browse code

depends treeio

GuangchuangYu authored on 20/12/2016 16:39:07
Showing 1 changed files
R/method-get-tree.R
History View file @ 817c093d
... ... 
@@ -1,90 +1,90 @@
1 
-##' @rdname get.tree-methods
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-##' @exportMethod get.tree
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-setMethod("get.tree", signature(object="apeBootstrap"),
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-          function(object,...) {
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-              object@phylo
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-          }
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-          )
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+## ##' @rdname get.tree-methods
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+## ##' @exportMethod get.tree
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+## setMethod("get.tree", signature(object="apeBootstrap"),
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+##           function(object,...) {
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+##               object@phylo
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+##           }
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+##           )
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-##' get.tree method
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-##'
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-##'
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-##' @docType methods
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-##' @name get.tree
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-##' @rdname get.tree-methods
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-##' @aliases get.tree,beast
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-##' @exportMethod get.tree
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-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
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-##' @usage get.tree(object, ...)
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-setMethod("get.tree", signature(object="beast"),
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-          function(object,...) {
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-              object@phylo
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-          }
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-          )
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+## ##' get.tree method
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+## ##'
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+## ##'
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+## ##' @docType methods
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+## ##' @name get.tree
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+## ##' @rdname get.tree-methods
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+## ##' @aliases get.tree,beast
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+## ##' @exportMethod get.tree
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+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
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+## ##' @usage get.tree(object, ...)
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+## setMethod("get.tree", signature(object="beast"),
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+##           function(object,...) {
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+##               object@phylo
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+##           }
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+##           )
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-##' @rdname get.tree-methods
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-##' @exportMethod get.tree
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-##' @param by one of rst or mlc
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-setMethod("get.tree", signature(object="codeml"),
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-          function(object, by="rst", ...) {
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-              if (by == "rst") {
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-                  return(object@rst@phylo)
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-              } else {
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-                  return(object@mlc@phylo)
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-              }
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-          })
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+## ##' @rdname get.tree-methods
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+## ##' @exportMethod get.tree
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+## ##' @param by one of rst or mlc
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+## setMethod("get.tree", signature(object="codeml"),
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+##           function(object, by="rst", ...) {
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+##               if (by == "rst") {
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+##                   return(object@rst@phylo)
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+##               } else {
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+##                   return(object@mlc@phylo)
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+##               }
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+##           })
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-##' @rdname get.tree-methods
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-##' @exportMethod get.tree
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-setMethod("get.tree", signature(object="jplace"),
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-          function(object) {
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-              object@phylo
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-          })
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+## ##' @rdname get.tree-methods
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+## ##' @exportMethod get.tree
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+## setMethod("get.tree", signature(object="jplace"),
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+##           function(object) {
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+##               object@phylo
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+##           })
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-##' @rdname get.tree-methods
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-##' @exportMethod get.tree
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-setMethod("get.tree", signature(object = "nhx"),
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-          function(object) {
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-              object@phylo
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-          }
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-          )
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+## ##' @rdname get.tree-methods
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+## ##' @exportMethod get.tree
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+## setMethod("get.tree", signature(object = "nhx"),
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+##           function(object) {
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+##               object@phylo
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+##           }
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+##           )
53 53
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-##' @rdname get.tree-methods
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-##' @exportMethod get.tree
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-setMethod("get.tree", signature(object="phylip"),
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-          function(object,...) {
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-              object@phylo
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-          }
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-          )
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+## ##' @rdname get.tree-methods
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+## ##' @exportMethod get.tree
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+## setMethod("get.tree", signature(object="phylip"),
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+##           function(object,...) {
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+##               object@phylo
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+##           }
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+##           )
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-##' @rdname get.tree-methods
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-##' @exportMethod get.tree
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-setMethod("get.tree", signature(object="phylo"),
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-          function(object, ...) {
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-              return(object)
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-          })
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+## ##' @rdname get.tree-methods
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+## ##' @exportMethod get.tree
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+## setMethod("get.tree", signature(object="phylo"),
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+##           function(object, ...) {
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+##               return(object)
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+##           })
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-##' @rdname get.tree-methods
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-##' @exportMethod get.tree
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-setMethod("get.tree", signature(object="data.frame"),
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-          function(object, ...) {
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-              edge <- object[, c("parent", "node")]
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-              i <- which(edge[,1] != 0 & edge[,1] != edge[,2])
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-              edge <- edge[i, ]
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-              edge.length <- object[i, "branch.length"]
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-              tip.label <- object[object[, "isTip"], "label"]
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-              phylo <- list(edge = as.matrix(edge),
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-                  edge.length = edge.length,
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-                  tip.label = tip.label)
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+## ##' @rdname get.tree-methods
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+## ##' @exportMethod get.tree
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+## setMethod("get.tree", signature(object="data.frame"),
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+##           function(object, ...) {
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+##               edge <- object[, c("parent", "node")]
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+##               i <- which(edge[,1] != 0 & edge[,1] != edge[,2])
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+##               edge <- edge[i, ]
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+##               edge.length <- object[i, "branch.length"]
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+##               tip.label <- object[object[, "isTip"], "label"]
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+##               phylo <- list(edge = as.matrix(edge),
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+##                   edge.length = edge.length,
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+##                   tip.label = tip.label)
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-              node.label <- object[!object[, "isTip"], "label"]
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-              if (!all(is.na(node.label))) {
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-                  phylo$node.label <- node.label
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-              }
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-              phylo$Nnode <- sum(!object[, "isTip"])
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-              class(phylo) <- "phylo"
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-              return(phylo)
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-          })
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+##               node.label <- object[!object[, "isTip"], "label"]
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+##               if (!all(is.na(node.label))) {
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+##                   phylo$node.label <- node.label
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+##               }
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+##               phylo$Nnode <- sum(!object[, "isTip"])
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+##               class(phylo) <- "phylo"
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+##               return(phylo)
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+##           })
90 90
Browse code

bug fixed of get.tree for data.frame

guangchuang yu authored on 14/12/2016 08:12:22
Showing 1 changed files
R/method-get-tree.R
History View file @ 1a0e6ac4
... ... 
@@ -65,20 +65,21 @@ setMethod("get.tree", signature(object="phylo"),
65 65 
           function(object, ...) {
66 66 
               return(object)
67 67 
           })
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-
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+
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 ##' @rdname get.tree-methods
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 ##' @exportMethod get.tree
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 setMethod("get.tree", signature(object="data.frame"),
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           function(object, ...) {
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+              edge <- object[, c("parent", "node")]
73 74 
               i <- which(edge[,1] != 0 & edge[,1] != edge[,2])
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               edge <- edge[i, ]
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               edge.length <- object[i, "branch.length"]
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-              tip.label <- object[object[, "isTip"], "label"]
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-              phylo <- list(edge = edge,
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+              tip.label <- object[object[, "isTip"], "label"]
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+              phylo <- list(edge = as.matrix(edge),
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                   edge.length = edge.length,
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                   tip.label = tip.label)
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-              node.label <- object[!object[, "isTip"], "label"]
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+              node.label <- object[!object[, "isTip"], "label"]
82 83 
               if (!all(is.na(node.label))) {
83 84 
                   phylo$node.label <- node.label
84 85 
               }
Browse code

merge

brj1 authored on 06/12/2016 18:37:15
Showing 0 changed files
Browse code

added get.tree method for data.frame

brj1 authored on 06/12/2016 18:18:47
Showing 1 changed files
R/method-get-tree.R
History View file @ e0430f69
... ... 
@@ -65,3 +65,24 @@ setMethod("get.tree", signature(object="phylo"),
65 65 
           function(object, ...) {
66 66 
               return(object)
67 67 
           })
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+
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+##' @rdname get.tree-methods
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+##' @exportMethod get.tree
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+setMethod("get.tree", signature(object="data.frame"),
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+          function(object, ...) {
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+              i <- which(edge[,1] != 0 & edge[,1] != edge[,2])
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+              edge <- edge[i, ]
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+              edge.length <- object[i, "branch.length"]
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+              tip.label <- object[object[, "isTip"], "label"]
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+              phylo <- list(edge = edge,
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+                  edge.length = edge.length,
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+                  tip.label = tip.label)
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+
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+              node.label <- object[!object[, "isTip"], "label"]
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+              if (!all(is.na(node.label))) {
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+                  phylo$node.label <- node.label
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+              }
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+              phylo$Nnode <- sum(!object[, "isTip"])
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+              class(phylo) <- "phylo"
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+              return(phylo)
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+          })
68 89 
\ No newline at end of file
Browse code

branch.length support phylo4d@data

guangchuang yu authored on 06/12/2016 05:42:11
Showing 1 changed files
R/method-get-tree.R
History View file @ 8d41c5d9
... ... 
@@ -65,3 +65,6 @@ setMethod("get.tree", signature(object="phylo"),
65 65 
           function(object, ...) {
66 66 
               return(object)
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           })
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+
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+
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+
Browse code

version 1.5.5

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@118092 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 02/06/2016 03:14:43
Showing 1 changed files
R/method-get-tree.R
History View file @ 328fdc06
... ... 
@@ -59,3 +59,9 @@ setMethod("get.tree", signature(object="phylip"),
59 59 
           }
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           )
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+##' @rdname get.tree-methods
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+##' @exportMethod get.tree
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+setMethod("get.tree", signature(object="phylo"),
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+          function(object, ...) {
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+              return(object)
67 
+          })
Browse code

support phylip format

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@112578 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 15/01/2016 04:55:05
Showing 1 changed files
R/method-get-tree.R
History View file @ 6f076280
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,61 @@
1 
+##' @rdname get.tree-methods
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+##' @exportMethod get.tree
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+setMethod("get.tree", signature(object="apeBootstrap"),
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+          function(object,...) {
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+              object@phylo
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+          }
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+          )
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+
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+##' get.tree method
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+##'
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+##'
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+##' @docType methods
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+##' @name get.tree
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+##' @rdname get.tree-methods
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+##' @aliases get.tree,beast
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+##' @exportMethod get.tree
17 
+##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
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+##' @usage get.tree(object, ...)
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+setMethod("get.tree", signature(object="beast"),
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+          function(object,...) {
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+              object@phylo
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+          }
23 
+          )
24 
+
25 
+
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+##' @rdname get.tree-methods
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+##' @exportMethod get.tree
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+##' @param by one of rst or mlc
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+setMethod("get.tree", signature(object="codeml"),
30 
+          function(object, by="rst", ...) {
31 
+              if (by == "rst") {
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+                  return(object@rst@phylo)
33 
+              } else {
34 
+                  return(object@mlc@phylo)
35 
+              }
36 
+          })
37 
+
38 
+
39 
+##' @rdname get.tree-methods
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+##' @exportMethod get.tree
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+setMethod("get.tree", signature(object="jplace"),
42 
+          function(object) {
43 
+              object@phylo
44 
+          })
45 
+
46 
+##' @rdname get.tree-methods
47 
+##' @exportMethod get.tree
48 
+setMethod("get.tree", signature(object = "nhx"),
49 
+          function(object) {
50 
+              object@phylo
51 
+          }
52 
+          )
53 
+
54 
+##' @rdname get.tree-methods
55 
+##' @exportMethod get.tree
56 
+setMethod("get.tree", signature(object="phylip"),
57 
+          function(object,...) {
58 
+              object@phylo
59 
+          }
60 
+          )
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+