fixed edge.length in get.tree.dataframe

DESCRIPTION

@@ -8,6 +8,8 @@ Authors@R: c(
 	   person("Justin", "Silverman", email = "[email protected]", rol = "ctb", comment = "geom_balance"),
 	   person("Casey", "Dunn", email = "[email protected]", rol = "ctb",
 	          comment = "NHX")
+           person("Bradley", "Jones", email = "[email protected]", rol = "ctb",
+	          comment = "get.tree method for data.frame")
 	   )
 Maintainer: Guangchuang Yu <[email protected]>
 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.

R/method-get-tree.R

@@ -70,9 +70,9 @@ setMethod("get.tree", signature(object="phylo"),
 ##' @exportMethod get.tree
 setMethod("get.tree", signature(object="data.frame"),
           function(object, ...) {
-              edge <- object[, c("parent", "node")]
-              edge <- edge[edge[,1] != 0 & edge[,1] != edge[,2], ]
-              edge.length <- object[, "branch.length"]
+              i <- which(edge[,1] != 0 & edge[,1] != edge[,2])
+              edge <- edge[i, ]
+              edge.length <- object[i, "branch.length"]
               tip.label <- object[object[, "isTip"], "label"] 
               phylo <- list(edge = edge,
                   edge.length = edge.length,