Browse code

depends treeio

GuangchuangYu authored on 20/12/2016 16:39:07
Showing 73 changed files

... ...
@@ -1,7 +1,7 @@
1 1
 Package: ggtree
2 2
 Type: Package
3 3
 Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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-Version: 1.7.4
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+Version: 1.7.5
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 Authors@R: c(
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 	   person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph")),
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 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = c("aut", "ths")),
... ...
@@ -11,8 +11,9 @@ Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
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 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.
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 	     'ggtree' is designed for visualization and annotation of phylogenetic trees with their covariates and other associated data.
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 Depends:
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-    R (>= 3.3.1),
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-    ggplot2 (>= 2.2.0)
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+    R (>= 3.3.2),
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+    ggplot2 (>= 2.2.0),
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+    treeio
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 Imports:
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     ape,
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     grDevices,
... ...
@@ -33,7 +33,6 @@ export(Date2decimal)
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 export(MRCA)
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 export(StatBalance)
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 export(StatHilight)
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-export(add_colorbar)
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 export(annotation_image)
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 export(apeBoot)
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 export(as.binary)
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@@ -41,7 +40,6 @@ export(as.polytomy)
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 export(collapse)
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 export(decimal2Date)
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 export(download.phylopic)
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-export(drop.tip)
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 export(expand)
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 export(facet_plot)
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 export(flip)
... ...
@@ -64,29 +62,17 @@ export(geom_tippoint)
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 export(geom_tree)
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 export(geom_tree2)
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 export(geom_treescale)
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-export(get.fields)
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 export(get.offspring.tip)
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 export(get.path)
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 export(get.phylopic)
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-export(get.placements)
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-export(get.subs)
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-export(get.tipseq)
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-export(get.tree)
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-export(get.treeinfo)
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-export(get.treetext)
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-export(getNodeNum)
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-export(getRoot)
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 export(get_balance_position)
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 export(get_clade_position)
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 export(get_heatmap_column_position)
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 export(get_taxa_name)
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 export(ggtree)
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 export(gheatmap)
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-export(groupClade)
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-export(groupOTU)
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 export(gzoom)
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 export(inset)
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-export(is.ggtree)
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 export(mask)
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 export(merge_tree)
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 export(msaplot)
... ...
@@ -95,32 +81,16 @@ export(nodebar)
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 export(nodeid)
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 export(nodepie)
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 export(open_tree)
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-export(phyPML)
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 export(phylopic)
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 export(plot)
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-export(pmlToSeq)
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 export(raxml2nwk)
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-export(read.baseml)
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-export(read.beast)
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-export(read.codeml)
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-export(read.codeml_mlc)
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-export(read.hyphy)
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-export(read.jplace)
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-export(read.nhx)
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-export(read.paml_rst)
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-export(read.phylip)
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 export(read.phyloT)
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-export(read.r8s)
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-export(read.raxml)
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-export(read.tree)
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 export(reroot)
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 export(rescale_tree)
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 export(revts)
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 export(rotate)
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 export(rotate_tree)
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-export(rtree)
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 export(scaleClade)
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-export(scale_color)
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 export(scale_x_ggtree)
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 export(stat_balance)
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 export(stat_hilight)
... ...
@@ -130,46 +100,20 @@ export(theme_transparent)
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 export(theme_tree)
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 export(theme_tree2)
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 export(viewClade)
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-export(write.jplace)
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 export(xlim_expand)
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 export(xlim_tree)
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-exportClasses(apeBootstrap)
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-exportClasses(beast)
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-exportClasses(codeml)
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-exportClasses(codeml_mlc)
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-exportClasses(hyphy)
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-exportClasses(jplace)
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-exportClasses(nhx)
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-exportClasses(paml_rst)
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-exportClasses(phangorn)
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-exportClasses(phylip)
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-exportClasses(r8s)
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-exportClasses(raxml)
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-exportMethods(drop.tip)
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-exportMethods(get.fields)
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-exportMethods(get.placements)
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-exportMethods(get.subs)
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-exportMethods(get.tipseq)
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-exportMethods(get.tree)
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-exportMethods(get.treeinfo)
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-exportMethods(get.treetext)
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 exportMethods(groupClade)
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 exportMethods(groupOTU)
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 exportMethods(gzoom)
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 exportMethods(plot)
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 exportMethods(reroot)
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-exportMethods(scale_color)
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-exportMethods(show)
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 importFrom(ape,di2multi)
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 importFrom(ape,extract.clade)
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 importFrom(ape,getMRCA)
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 importFrom(ape,is.binary.tree)
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 importFrom(ape,ladderize)
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-importFrom(ape,print.phylo)
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-importFrom(ape,read.nexus)
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 importFrom(ape,read.tree)
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 importFrom(ape,reorder.phylo)
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-importFrom(ape,which.edge)
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 importFrom(ape,write.tree)
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 importFrom(ggplot2,GeomCurve)
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 importFrom(ggplot2,GeomLabel)
... ...
@@ -235,20 +179,15 @@ importFrom(grid,pushViewport)
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 importFrom(grid,rasterGrob)
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 importFrom(grid,unit)
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 importFrom(grid,viewport)
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-importFrom(jsonlite,fromJSON)
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 importFrom(magrittr,"%<>%")
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 importFrom(magrittr,"%>%")
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 importFrom(magrittr,add)
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 importFrom(magrittr,equals)
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-importFrom(methods,"slot<-")
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-importFrom(methods,.hasSlot)
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-importFrom(methods,is)
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-importFrom(methods,missingArg)
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-importFrom(methods,new)
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-importFrom(methods,show)
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-importFrom(methods,slot)
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 importFrom(stats4,plot)
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 importFrom(tidyr,gather)
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+importFrom(treeio,as.treedata)
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+importFrom(treeio,groupClade)
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+importFrom(treeio,groupOTU)
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 importFrom(utils,download.file)
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 importFrom(utils,modifyList)
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 importFrom(utils,packageDescription)
... ...
@@ -1,3 +1,7 @@
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+CHANGES IN VERSION 1.7.5
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+------------------------
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+ o remove codes that move to treeio and now ggtree depends treeio <2016-12-20, Tue>
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+ 
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 CHANGES IN VERSION 1.7.4
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 ------------------------
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  o is.ggtree function to test whether object is produced by ggtree <2016-12-06, Tue>
... ...
@@ -1,9 +1,9 @@
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-setOldClass("phylo")
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-setOldClass("multiPhylo")
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-setOldClass("ggtree")
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+## setOldClass("phylo")
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+## setOldClass("multiPhylo")
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+## setOldClass("ggtree")
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5 5
 
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-setClassUnion("phyloOrmultiPhylo", c("phylo", "multiPhylo"))
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+## setClassUnion("phyloOrmultiPhylo", c("phylo", "multiPhylo"))
7 7
 
8 8
 
9 9
 supported_tree_object <- function() {
... ...
@@ -21,367 +21,367 @@ supported_tree_object <- function() {
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       "raxml")
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 }
23 23
 
24
-##' Class "apeBootstrap"
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-##' This class stores ape bootstrapping analysis result
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-##'
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-##'
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-##' @name apeBootstrap-class
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-##' @docType class
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-##' @slot phylo phylo object of treetext
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-##' @slot fields available features
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-##' @slot bootstrap bootstrap value
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-##' @slot extraInfo extra information
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-##' @exportClass apeBootstrap
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-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
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-##' @keywords classes
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-setClass("apeBootstrap",
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-         representation = representation(
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-             phylo = "phylo",
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-             fields = "character",
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-             bootstrap = "data.frame",
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-             extraInfo = "data.frame"
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-         )
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-         )
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+## ##' Class "apeBootstrap"
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+## ##' This class stores ape bootstrapping analysis result
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+## ##'
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+## ##'
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+## ##' @name apeBootstrap-class
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+## ##' @docType class
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+## ##' @slot phylo phylo object of treetext
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+## ##' @slot fields available features
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+## ##' @slot bootstrap bootstrap value
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+## ##' @slot extraInfo extra information
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+## ##' @exportClass apeBootstrap
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+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
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+## ##' @keywords classes
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+## setClass("apeBootstrap",
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+##          representation = representation(
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+##              phylo = "phylo",
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+##              fields = "character",
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+##              bootstrap = "data.frame",
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+##              extraInfo = "data.frame"
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+##          )
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+##          )
45 45
 
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-##' Class "beast"
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-##' This class stores information of beast output
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-##'
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-##'
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-##' @name beast-class
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-##' @aliases beast-class
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-##'      get.tree,beast-method
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-##'
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-##' @docType class
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-##' @slot fields beast statistic variables
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-##' @slot treetext tree text in beast file
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-##' @slot phylo tree phylo object
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-##' @slot translation tip number to name translation in beast file
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-##' @slot stats beast statistics
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-##' @slot file beast file, nexus format
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-##' @slot extraInfo extra information
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-##' @exportClass beast
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-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
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-##' @seealso \code{\link{show}} \code{\link{get.fields}}
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-##'           \code{\link{ggtree}}
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-##' @keywords classes
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-setClass("beast",
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-         representation  = representation(
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-             fields      = "character",
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-             treetext    = "character",
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-             phylo       = "phylo",
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-             translation = "matrix",
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-             stats       = "data.frame",
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-             file        = "character",
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-             extraInfo   = "data.frame"
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-             )
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-         )
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+## ##' Class "beast"
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+## ##' This class stores information of beast output
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+## ##'
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+## ##'
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+## ##' @name beast-class
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+## ##' @aliases beast-class
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+## ##'      get.tree,beast-method
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+## ##'
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+## ##' @docType class
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+## ##' @slot fields beast statistic variables
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+## ##' @slot treetext tree text in beast file
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+## ##' @slot phylo tree phylo object
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+## ##' @slot translation tip number to name translation in beast file
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+## ##' @slot stats beast statistics
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+## ##' @slot file beast file, nexus format
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+## ##' @slot extraInfo extra information
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+## ##' @exportClass beast
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+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
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+## ##' @seealso \code{\link{show}} \code{\link{get.fields}}
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+## ##'           \code{\link{ggtree}}
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+## ##' @keywords classes
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+## setClass("beast",
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+##          representation  = representation(
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+##              fields      = "character",
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+##              treetext    = "character",
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+##              phylo       = "phylo",
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+##              translation = "matrix",
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+##              stats       = "data.frame",
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+##              file        = "character",
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+##              extraInfo   = "data.frame"
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+##              )
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+##          )
78 78
 
79 79
 
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-##' Class "codeml_mlc"
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-##' This class stores information of mlc file frm codeml output
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-##'
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-##'
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-##' @name codeml_mlc-class
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-##' @docType class
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-##' @slot fields available features
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-##' @slot treetext tree text
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-##' @slot phylo phylo object
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-##' @slot dNdS dN dS information
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-##' @slot mlcfile mlc file
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-##' @slot extraInfo extra information
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-##' @exportClass codeml_mlc
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-##' @author Guangchuang Yu
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-##' @seealso \linkS4class{paml_rst} \linkS4class{codeml}
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-##' @keywords classes
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-setClass("codeml_mlc",
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-         representation = representation(
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-             fields     = "character",
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-             treetext   = "character",
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-             phylo      = "phylo",
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-             dNdS       = "matrix",
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-             ## seq_type   = "character",
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-             ## tip_seq    = "character",
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-             mlcfile    = "character",
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-             extraInfo  = "data.frame"
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-             )
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-         )
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+## ##' Class "codeml_mlc"
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+## ##' This class stores information of mlc file frm codeml output
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+## ##'
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+## ##'
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+## ##' @name codeml_mlc-class
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+## ##' @docType class
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+## ##' @slot fields available features
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+## ##' @slot treetext tree text
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+## ##' @slot phylo phylo object
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+## ##' @slot dNdS dN dS information
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+## ##' @slot mlcfile mlc file
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+## ##' @slot extraInfo extra information
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+## ##' @exportClass codeml_mlc
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+## ##' @author Guangchuang Yu
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+## ##' @seealso \linkS4class{paml_rst} \linkS4class{codeml}
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+## ##' @keywords classes
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+## setClass("codeml_mlc",
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+##          representation = representation(
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+##              fields     = "character",
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+##              treetext   = "character",
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+##              phylo      = "phylo",
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+##              dNdS       = "matrix",
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+##              ## seq_type   = "character",
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+##              ## tip_seq    = "character",
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+##              mlcfile    = "character",
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+##              extraInfo  = "data.frame"
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+##              )
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+##          )
108 108
 
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-##' Class "paml_rst"
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-##' This class stores information of rst file from PAML output
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-##'
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-##'
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-##' @name paml_rst-class
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-##' @aliases paml_rst-class
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-##'   set.subs,paml_rst-method
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-##'   set.subs<-,paml_rst-method
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-##'
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-##' @docType class
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-##' @slot fields availabel attributes
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-##' @slot treetext tree text
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-##' @slot phylo phylo object
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-##' @slot seq_type one of "NT" and "AA"
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-##' @slot tip_seq sequences of tips
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-##' @slot marginal_ancseq Marginal reconstruction of ancestral sequences
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-##' @slot joint_ancseq Joint reconstruction of ancestral sequences
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-##' @slot marginal_subs sequence substitutions based on marginal_ancseq
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-##' @slot joint_subs sequence substitutions based on joint_ancseq
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-##' @slot marginal_AA_subs Amino acid sequence substitutions based on marginal_ancseq
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-##' @slot joint_AA_subs Amino acid sequence substitutions based on joint_ancseq
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-##' @slot rstfile rst file
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-##' @slot extraInfo extra information
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-##' @exportClass paml_rst
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-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
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-##' @seealso \linkS4class{codeml} \linkS4class{codeml_mlc}
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-##' @keywords classes
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-setClass("paml_rst",
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-         representation       = representation(
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-             fields           = "character",
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-             treetext         = "character",
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-             phylo            = "phylo",
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-             seq_type         = "character",
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-             tip_seq          = "character",
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-             marginal_ancseq  = "character",
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-             joint_ancseq     = "character",
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-             marginal_subs    = "data.frame",
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-             joint_subs       = "data.frame",
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-             marginal_AA_subs = "data.frame",
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-             joint_AA_subs    = "data.frame",
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-             rstfile          = "character",
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-             extraInfo        = "data.frame"
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-         )
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-         )
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+## ##' Class "paml_rst"
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+## ##' This class stores information of rst file from PAML output
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+## ##'
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+## ##'
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+## ##' @name paml_rst-class
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+## ##' @aliases paml_rst-class
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+## ##'   set.subs,paml_rst-method
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+## ##'   set.subs<-,paml_rst-method
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+## ##'
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+## ##' @docType class
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+## ##' @slot fields availabel attributes
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+## ##' @slot treetext tree text
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+## ##' @slot phylo phylo object
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+## ##' @slot seq_type one of "NT" and "AA"
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+## ##' @slot tip_seq sequences of tips
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+## ##' @slot marginal_ancseq Marginal reconstruction of ancestral sequences
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+## ##' @slot joint_ancseq Joint reconstruction of ancestral sequences
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+## ##' @slot marginal_subs sequence substitutions based on marginal_ancseq
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+## ##' @slot joint_subs sequence substitutions based on joint_ancseq
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+## ##' @slot marginal_AA_subs Amino acid sequence substitutions based on marginal_ancseq
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+## ##' @slot joint_AA_subs Amino acid sequence substitutions based on joint_ancseq
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+## ##' @slot rstfile rst file
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+## ##' @slot extraInfo extra information
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+## ##' @exportClass paml_rst
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+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
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+## ##' @seealso \linkS4class{codeml} \linkS4class{codeml_mlc}
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+## ##' @keywords classes
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+## setClass("paml_rst",
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+##          representation       = representation(
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+##              fields           = "character",
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+##              treetext         = "character",
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+##              phylo            = "phylo",
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+##              seq_type         = "character",
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+##              tip_seq          = "character",
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+##              marginal_ancseq  = "character",
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+##              joint_ancseq     = "character",
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+##              marginal_subs    = "data.frame",
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+##              joint_subs       = "data.frame",
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+##              marginal_AA_subs = "data.frame",
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+##              joint_AA_subs    = "data.frame",
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+##              rstfile          = "character",
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+##              extraInfo        = "data.frame"
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+##          )
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+##          )
153 153
 
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-##' Class "codeml"
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-##' This class stores information of output from codeml
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-##'
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-##'
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-##' @name codeml-class
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-##' @docType class
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-##' @slot mlc A \code{code_mlc} object
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-##' @slot rst A \code{paml_rst} object
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-##' @slot extraInfo extra information
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-##' @exportClass codeml
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-##' @seealso \linkS4class{codeml_mlc} \linkS4class{paml_rst}
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-##' @keywords codeml
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-setClass("codeml",
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-         representation = representation(
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-             mlc       = "codeml_mlc",
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-             rst       = "paml_rst",
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-             extraInfo = "data.frame"
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-             )
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-         )
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+## ##' Class "codeml"
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+## ##' This class stores information of output from codeml
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+## ##'
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+## ##'
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+## ##' @name codeml-class
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+## ##' @docType class
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+## ##' @slot mlc A \code{code_mlc} object
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+## ##' @slot rst A \code{paml_rst} object
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+## ##' @slot extraInfo extra information
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+## ##' @exportClass codeml
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+## ##' @seealso \linkS4class{codeml_mlc} \linkS4class{paml_rst}
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+## ##' @keywords codeml
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+## setClass("codeml",
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+##          representation = representation(
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+##              mlc       = "codeml_mlc",
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+##              rst       = "paml_rst",
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+##              extraInfo = "data.frame"
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+##              )
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+##          )
173 173
 
174 174
 
175 175
 
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-##' Class "hyphy"
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-##' This class stores information of HYPHY output
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-##'
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-##'
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-##' @name hyphy-class
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-##' @docType class
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-##' @slot fields available features
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-##' @slot treetext tree text
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-##' @slot phylo phylo object
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-##' @slot seq_type one of "NT" and "AA"
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-##' @slot subs sequence substitutions
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-##' @slot AA_subs Amino acid sequence substitution
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-##' @slot ancseq ancestral sequences
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-##' @slot tip_seq tip sequences
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-##' @slot tip.fasfile fasta file of tip sequences
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-##' @slot tree.file tree file
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-##' @slot ancseq.file ancestral sequence file, nexus format
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-##' @slot extraInfo extra information
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-##' @exportClass hyphy
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-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
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-##' @seealso \linkS4class{paml_rst}
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-##' @keywords classes
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-setClass("hyphy",
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-         representation  = representation(
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-             fields      = "character",
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-             treetext    = "character",
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-             phylo       = "phylo",
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-             seq_type    = "character",
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-             subs        = "data.frame",
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-             AA_subs     = "data.frame",
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-             ancseq      = "character",
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-             tip_seq     = "character",
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-             tip.fasfile = "character",
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-             tree.file   = "character",
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-             ancseq.file = "character",
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-             extraInfo   = "data.frame"
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-             )
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-         )
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+## ##' Class "hyphy"
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+## ##' This class stores information of HYPHY output
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+## ##'
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+## ##'
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+## ##' @name hyphy-class
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+## ##' @docType class
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+## ##' @slot fields available features
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+## ##' @slot treetext tree text
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+## ##' @slot phylo phylo object
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+## ##' @slot seq_type one of "NT" and "AA"
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+## ##' @slot subs sequence substitutions
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+## ##' @slot AA_subs Amino acid sequence substitution
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+## ##' @slot ancseq ancestral sequences
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+## ##' @slot tip_seq tip sequences
190
+## ##' @slot tip.fasfile fasta file of tip sequences
191
+## ##' @slot tree.file tree file
192
+## ##' @slot ancseq.file ancestral sequence file, nexus format
193
+## ##' @slot extraInfo extra information
194
+## ##' @exportClass hyphy
195
+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
196
+## ##' @seealso \linkS4class{paml_rst}
197
+## ##' @keywords classes
198
+## setClass("hyphy",
199
+##          representation  = representation(
200
+##              fields      = "character",
201
+##              treetext    = "character",
202
+##              phylo       = "phylo",
203
+##              seq_type    = "character",
204
+##              subs        = "data.frame",
205
+##              AA_subs     = "data.frame",
206
+##              ancseq      = "character",
207
+##              tip_seq     = "character",
208
+##              tip.fasfile = "character",
209
+##              tree.file   = "character",
210
+##              ancseq.file = "character",
211
+##              extraInfo   = "data.frame"
212
+##              )
213
+##          )
214 214
 
215
-##' Class "jplace"
216
-##' This class stores information of jplace file.
217
-##'
218
-##'
219
-##' @name jplace-class
220
-##' @aliases jplace-class
221
-##'   show,jplace-method
222
-##'   get.placements,jplace-method
223
-##'   get.treeinfo,jplace-method
224
-##'   get.fields,jplace-method
225
-##'   get.treetext,jplace-method
226
-##'
227
-##' @docType class
228
-##' @slot fields colnames of first variable of placements
229
-##' @slot treetext tree text
230
-##' @slot phylo tree phylo object
231
-##' @slot placements placement information
232
-##' @slot version version
233
-##' @slot metadata metadata
234
-##' @slot file jplace file
235
-##' @slot extraInfo extra information
236
-##' @exportClass jplace
237
-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
238
-##' @seealso \code{\link{show}} \code{\link{get.tree}}
239
-##'          \code{\link{ggtree}}
240
-##' @keywords classes
241
-setClass("jplace",
242
-         representation = representation(
243
-             fields     = "character",
244
-             treetext   = "character",
245
-             phylo      = "phylo",
246
-             placements = "data.frame",
247
-             version    = "numeric",
248
-             metadata   = "list",
249
-             file       = "character",
250
-             extraInfo  = "data.frame"
251
-             )
252
-         )
215
+## ##' Class "jplace"
216
+## ##' This class stores information of jplace file.
217
+## ##'
218
+## ##'
219
+## ##' @name jplace-class
220
+## ##' @aliases jplace-class
221
+## ##'   show,jplace-method
222
+## ##'   get.placements,jplace-method
223
+## ##'   get.treeinfo,jplace-method
224
+## ##'   get.fields,jplace-method
225
+## ##'   get.treetext,jplace-method
226
+## ##'
227
+## ##' @docType class
228
+## ##' @slot fields colnames of first variable of placements
229
+## ##' @slot treetext tree text
230
+## ##' @slot phylo tree phylo object
231
+## ##' @slot placements placement information
232
+## ##' @slot version version
233
+## ##' @slot metadata metadata
234
+## ##' @slot file jplace file
235
+## ##' @slot extraInfo extra information
236
+## ##' @exportClass jplace
237
+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
238
+## ##' @seealso \code{\link{show}} \code{\link{get.tree}}
239
+## ##'          \code{\link{ggtree}}
240
+## ##' @keywords classes
241
+## setClass("jplace",
242
+##          representation = representation(
243
+##              fields     = "character",
244
+##              treetext   = "character",
245
+##              phylo      = "phylo",
246
+##              placements = "data.frame",
247
+##              version    = "numeric",
248
+##              metadata   = "list",
249
+##              file       = "character",
250
+##              extraInfo  = "data.frame"
251
+##              )
252
+##          )
253 253
 
254 254
 
255
-##' Class "nhx"
256
-##' This class stores nhx tree
257
-##'
258
-##'
259
-##' @name nhx-class
260
-##' @rdname nhx-class
261
-##' @docType class
262
-##' @slot file input file
263
-##' @slot fields available feature
264
-##' @slot phylo phylo object
265
-##' @slot nhx_tags tag information in nhx file
266
-##' @slot extraInfo extra information
267
-##' @exportClass nhx
268
-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
269
-##' @keywords classes
270
-setClass("nhx",
271
-         representation = representation(
272
-             file = "character",
273
-             fields = "character",
274
-             phylo = "phylo",
275
-             nhx_tags = "data.frame",
276
-             extraInfo = "data.frame"
277
-         )
278
-         )
255
+## ##' Class "nhx"
256
+## ##' This class stores nhx tree
257
+## ##'
258
+## ##'
259
+## ##' @name nhx-class
260
+## ##' @rdname nhx-class
261
+## ##' @docType class
262
+## ##' @slot file input file
263
+## ##' @slot fields available feature
264
+## ##' @slot phylo phylo object
265
+## ##' @slot nhx_tags tag information in nhx file
266
+## ##' @slot extraInfo extra information
267
+## ##' @exportClass nhx
268
+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
269
+## ##' @keywords classes
270
+## setClass("nhx",
271
+##          representation = representation(
272
+##              file = "character",
273
+##              fields = "character",
274
+##              phylo = "phylo",
275
+##              nhx_tags = "data.frame",
276
+##              extraInfo = "data.frame"
277
+##          )
278
+##          )
279 279
 
280 280
 
281
-##' Class "phangorn"
282
-##' This class stores ancestral sequences inferred from 'phangorn'
283
-##'
284
-##'
285
-##' @name phangorn-class
286
-##' @docType class
287
-##' @slot fields available attributes
288
-##' @slot phylo phylo object
289
-##' @slot seq_type one of "NT" and "AA"
290
-##' @slot tip_seq sequences of tips
291
-##' @slot ancseq ancenstral sequences
292
-##' @slot subs sequence substitution
293
-##' @slot AA_subs Amino acid sequence substitution
294
-##' @slot extraInfo extra information
295
-##' @exportClass phangorn
296
-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
297
-##' @seealso \linkS4class{paml_rst}
298
-##' @keywords classes
299
-setClass("phangorn",
300
-         representation = representation(
301
-             fields = "character",
302
-             phylo = "phylo",
303
-             seq_type = "character",
304
-             tip_seq = "character",
305
-             ancseq = "character",
306
-             subs = "data.frame",
307
-             AA_subs = "data.frame",
308
-             extraInfo = "data.frame")
309
-         )
281
+## ##' Class "phangorn"
282
+## ##' This class stores ancestral sequences inferred from 'phangorn'
283
+## ##'
284
+## ##'
285
+## ##' @name phangorn-class
286
+## ##' @docType class
287
+## ##' @slot fields available attributes
288
+## ##' @slot phylo phylo object
289
+## ##' @slot seq_type one of "NT" and "AA"
290
+## ##' @slot tip_seq sequences of tips
291
+## ##' @slot ancseq ancenstral sequences
292
+## ##' @slot subs sequence substitution
293
+## ##' @slot AA_subs Amino acid sequence substitution
294
+## ##' @slot extraInfo extra information
295
+## ##' @exportClass phangorn
296
+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
297
+## ##' @seealso \linkS4class{paml_rst}
298
+## ##' @keywords classes
299
+## setClass("phangorn",
300
+##          representation = representation(
301
+##              fields = "character",
302
+##              phylo = "phylo",
303
+##              seq_type = "character",
304
+##              tip_seq = "character",
305
+##              ancseq = "character",
306
+##              subs = "data.frame",
307
+##              AA_subs = "data.frame",
308
+##              extraInfo = "data.frame")
309
+##          )
310 310
 
311 311
 
312 312
 
313
-##' Class "phylip"
314
-##' This class stores phylip tree(s)
315
-##'
316
-##'
317
-##' @name phylip-class
318
-##' @docType class
319
-##' @slot file input file
320
-##' @slot fields available feature
321
-##' @slot phylo phylo or multiPhylo
322
-##' @slot ntree number of trees
323
-##' @slot sequence sequences
324
-##' @slot extraInfo extra information
325
-##' @exportClass phylip
326
-##' @author Guangchuang Yu
327
-##' @keywords classes
328
-setClass("phylip",
329
-         representation = representation(
330
-             file = "character",
331
-             fields = "character",
332
-             phylo = "phyloOrmultiPhylo",
333
-             ntree = "numeric",
334
-             sequence = "character",
335
-             extraInfo = "data.frame")
336
-         )
313
+## ##' Class "phylip"
314
+## ##' This class stores phylip tree(s)
315
+## ##'
316
+## ##'
317
+## ##' @name phylip-class
318
+## ##' @docType class
319
+## ##' @slot file input file
320
+## ##' @slot fields available feature
321
+## ##' @slot phylo phylo or multiPhylo
322
+## ##' @slot ntree number of trees
323
+## ##' @slot sequence sequences
324
+## ##' @slot extraInfo extra information
325
+## ##' @exportClass phylip
326
+## ##' @author Guangchuang Yu
327
+## ##' @keywords classes
328
+## setClass("phylip",
329
+##          representation = representation(
330
+##              file = "character",
331
+##              fields = "character",
332
+##              phylo = "phyloOrmultiPhylo",
333
+##              ntree = "numeric",
334
+##              sequence = "character",
335
+##              extraInfo = "data.frame")
336
+##          )
337 337
 
338 338
 
339
-##' Class "r8s"
340
-##' This class stores output info from r8s
341
-##'
342
-##'
343
-##' @name r8s-class
344
-##' @docType class
345
-##' @slot file input file
346
-##' @slot fields available feature
347
-##' @slot treetext tree text
348
-##' @slot phylo multiPhylo, time tree, rate tree and absolute substitution tree
349
-##' @slot extraInfo extra information
350
-##' @exportClass r8s
351
-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
352
-##' @keywords classes
353
-setClass("r8s",
354
-         representation = representation(
355
-             file      = "character",
356
-             fields    = "character",
357
-             treetext  = "character",
358
-             phylo     = "multiPhylo",
359
-             extraInfo = "data.frame"
360
-             )
361
-         )
339
+## ##' Class "r8s"
340
+## ##' This class stores output info from r8s
341
+## ##'
342
+## ##'
343
+## ##' @name r8s-class
344
+## ##' @docType class
345
+## ##' @slot file input file
346
+## ##' @slot fields available feature
347
+## ##' @slot treetext tree text
348
+## ##' @slot phylo multiPhylo, time tree, rate tree and absolute substitution tree
349
+## ##' @slot extraInfo extra information
350
+## ##' @exportClass r8s
351
+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
352
+## ##' @keywords classes
353
+## setClass("r8s",
354
+##          representation = representation(
355
+##              file      = "character",
356
+##              fields    = "character",
357
+##              treetext  = "character",
358
+##              phylo     = "multiPhylo",
359
+##              extraInfo = "data.frame"
360
+##              )
361
+##          )
362 362
 
363 363
 
364
-##' Class "raxml"
365
-##' This class stores RAxML bootstrapping analysis result
366
-##'
367
-##'
368
-##' @name raxml-class
369
-##' @docType class
370
-##' @slot file input file
371
-##' @slot fields available features
372
-##' @slot treetext tree text
373
-##' @slot phylo phylo object of treetext
374
-##' @slot bootstrap bootstrap value
375
-##' @slot extraInfo extra information
376
-##' @exportClass raxml
377
-##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
378
-##' @keywords classes
379
-setClass("raxml",
380
-         representation = representation(
381
-             file       = "character",
382
-             treetext   = "character"
383
-         ),
384
-         contains = "apeBootstrap"
385
-         )
364
+## ##' Class "raxml"
365
+## ##' This class stores RAxML bootstrapping analysis result
366
+## ##'
367
+## ##'
368
+## ##' @name raxml-class
369
+## ##' @docType class
370
+## ##' @slot file input file
371
+## ##' @slot fields available features
372
+## ##' @slot treetext tree text
373
+## ##' @slot phylo phylo object of treetext
374
+## ##' @slot bootstrap bootstrap value
375
+## ##' @slot extraInfo extra information
376
+## ##' @exportClass raxml
377
+## ##' @author Guangchuang Yu \url{http://guangchuangyu.github.io}
378
+## ##' @keywords classes
379
+## setClass("raxml",
380
+##          representation = representation(
381
+##              file       = "character",
382
+##              treetext   = "character"
383
+##          ),
384
+##          contains = "apeBootstrap"
385
+##          )
386 386
 
387 387
 
... ...
@@ -33,124 +33,124 @@ if ( !isGeneric("plot") )
33 33
 ##' @export
34 34
 setGeneric("reroot", function(object, node, ...) standardGeneric("reroot"))
35 35
 
36
-##' @docType methods
37
-##' @name get.tree
38
-##' @rdname get.tree-methods
39
-##' @title get.tree method
40
-##' @param object one of \code{phylo}, \code{jplace}, \code{nhx}, \code{phangorn}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object
41
-##' @param ... additional parameter
42
-##' @return phylo object
43
-##' @export
44
-setGeneric("get.tree", function(object, ...) standardGeneric("get.tree"))
45
-
46
-##' @docType methods
47
-##' @name get.treetext
48
-##' @rdname get.treetext-methods
49
-##' @title get.treetext method
50
-##' @param object one of \code{phylo}, \code{jplace}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object
51
-##' @param ... additional parameter
52
-##' @return phylo object
53
-##' @export
54
-setGeneric("get.treetext", function(object, ...) standardGeneric("get.treetext"))
55
-
56
-
57
-##' @docType methods
58
-##' @name get.treeinfo
59
-##' @rdname get.treeinfo-methods
60
-##' @title get.treeinfo method
61
-##' @param object jplace object
62
-##' @param layout layout
63
-##' @param ladderize ladderize, logical
64
-##' @param right logical, parameter for ladderize
65
-##' @param ... additional parameter
66
-##' @return data.frame
67
-##' @export
68
-setGeneric("get.treeinfo", function(object, layout="phylogram", ladderize=TRUE, right=FALSE, ...) standardGeneric("get.treeinfo"))
69
-
70
-
71
-##' @docType methods
72
-##' @name get.fields
73
-##' @rdname get.fields-methods
74
-##' @title get.fields method
75
-##' @param object one of \code{jplace}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object
76
-##' @param ... additional parameter
77
-##' @return available annotation variables
78
-##' @export
79
-setGeneric("get.fields", function(object, ...) standardGeneric("get.fields"))
80
-
81
-
82
-##' @docType methods
83
-##' @name get.placements
84
-##' @rdname get.placements-methods
85
-##' @title get.placements method
86
-##' @param object jplace object
87
-##' @param by get best hit or others
88
-##' @param ... additional parameter
89
-##' @return data.frame
90
-##' @export
91
-setGeneric("get.placements", function(object, by, ...) standardGeneric("get.placements"))
92
-
93
-##' @docType methods
94
-##' @name get.subs
95
-##' @rdname get.subs-methods
96
-##' @title get.subs method
97
-##' @param object paml_rst object
98
-##' @param type one of 'marginal_subs', 'marginal_AA_subs',
99
-##'                     'joint_subs' or 'joint_AA_subs'.
100
-##' @param ... additional parameter
101
-##' @return data.frame
102
-##' @export
103
-setGeneric("get.subs", function(object, type, ...) standardGeneric("get.subs"))
104
-
105
-
106
-##' @docType methods
107
-##' @name get.tipseq
108
-##' @rdname get.tipseq-methods
109
-##' @title get.tipseq method
110
-##' @param object one of paml_rst or codeml object
111
-##' @param ... additional parameter
112
-##' @return character
113
-##' @export
114
-setGeneric("get.tipseq", function(object, ...) standardGeneric("get.tipseq"))
115
-
116
-##' @docType methods
117
-##' @name groupOTU
118
-##' @rdname groupOTU-methods
119
-##' @title groupOTU method
120
-##' @param object supported objects, including phylo, paml_rst,
121
-##'               codeml_mlc, codeml, jplace, beast, hyphy
122
-##' @param focus a vector of tip (label or number) or a list of tips.
123
-##' @param group_name name of the group, 'group' by default
124
-##' @param ... additional parameter
125
-##' @return group index
126
-##' @export
127
-setGeneric("groupOTU", function(object, focus, group_name="group", ...) standardGeneric("groupOTU"))
128
-
129
-##' @docType methods
130
-##' @name groupClade
131
-##' @rdname groupClade-methods
132
-##' @title groupClade method
133
-##' @param object supported objects, including phylo, paml_rst,
134
-##'               codeml_mlc, codeml, jplace, beast, hyphy
135
-##' @param node a internal node or a vector of internal nodes
136
-##' @param group_name name of the group, 'group' by default
137
-##' @param ... additional parameter
138
-##' @return group index
139
-##' @export
140
-setGeneric("groupClade", function(object, node, group_name="group", ...) standardGeneric("groupClade"))
141
-
142
-
143
-##' @docType methods
144
-##' @name scale_color
145
-##' @rdname scale_color-methods
146
-##' @title scale_color method
147
-##' @param object supported objects, including phylo, paml_rst,
148
-##'               codeml_mlc, codeml, jplace, beast, hyphy
149
-##' @param by one of numerical attributes
150
-##' @param ... additional parameter
151
-##' @return color vector
152
-##' @export
153
-setGeneric("scale_color", function(object, by, ...) standardGeneric("scale_color"))
36
+## ##' @docType methods
37
+## ##' @name get.tree
38
+## ##' @rdname get.tree-methods
39
+## ##' @title get.tree method
40
+## ##' @param object one of \code{phylo}, \code{jplace}, \code{nhx}, \code{phangorn}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object
41
+## ##' @param ... additional parameter
42
+## ##' @return phylo object
43
+## ##' @export
44
+## setGeneric("get.tree", function(object, ...) standardGeneric("get.tree"))
45
+
46
+## ##' @docType methods
47
+## ##' @name get.treetext
48
+## ##' @rdname get.treetext-methods
49
+## ##' @title get.treetext method
50
+## ##' @param object one of \code{phylo}, \code{jplace}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object
51
+## ##' @param ... additional parameter
52
+## ##' @return phylo object
53
+## ##' @export
54
+## setGeneric("get.treetext", function(object, ...) standardGeneric("get.treetext"))
55
+
56
+
57
+## ##' @docType methods
58
+## ##' @name get.treeinfo
59
+## ##' @rdname get.treeinfo-methods
60
+## ##' @title get.treeinfo method
61
+## ##' @param object jplace object
62
+## ##' @param layout layout
63
+## ##' @param ladderize ladderize, logical
64
+## ##' @param right logical, parameter for ladderize
65
+## ##' @param ... additional parameter
66
+## ##' @return data.frame
67
+## ##' @export
68
+## setGeneric("get.treeinfo", function(object, layout="phylogram", ladderize=TRUE, right=FALSE, ...) standardGeneric("get.treeinfo"))
69
+
70
+
71
+## ##' @docType methods
72
+## ##' @name get.fields
73
+## ##' @rdname get.fields-methods
74
+## ##' @title get.fields method
75
+## ##' @param object one of \code{jplace}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object
76
+## ##' @param ... additional parameter
77
+## ##' @return available annotation variables
78
+## ##' @export
79
+## setGeneric("get.fields", function(object, ...) standardGeneric("get.fields"))
80
+
81
+
82
+## ##' @docType methods
83
+## ##' @name get.placements
84
+## ##' @rdname get.placements-methods
85
+## ##' @title get.placements method
86
+## ##' @param object jplace object
87
+## ##' @param by get best hit or others
88
+## ##' @param ... additional parameter
89
+## ##' @return data.frame
90
+## ##' @export
91
+## setGeneric("get.placements", function(object, by, ...) standardGeneric("get.placements"))
92
+
93
+## ##' @docType methods
94
+## ##' @name get.subs
95
+## ##' @rdname get.subs-methods
96
+## ##' @title get.subs method
97
+## ##' @param object paml_rst object
98
+## ##' @param type one of 'marginal_subs', 'marginal_AA_subs',
99
+## ##'                     'joint_subs' or 'joint_AA_subs'.
100
+## ##' @param ... additional parameter
101
+## ##' @return data.frame
102
+## ##' @export
103
+## setGeneric("get.subs", function(object, type, ...) standardGeneric("get.subs"))
104
+
105
+
106
+## ##' @docType methods
107
+## ##' @name get.tipseq
108
+## ##' @rdname get.tipseq-methods
109
+## ##' @title get.tipseq method
110
+## ##' @param object one of paml_rst or codeml object
111
+## ##' @param ... additional parameter
112
+## ##' @return character
113
+## ##' @export
114
+## setGeneric("get.tipseq", function(object, ...) standardGeneric("get.tipseq"))
115
+
116
+## ##' @docType methods
117
+## ##' @name groupOTU
118
+## ##' @rdname groupOTU-methods
119
+## ##' @title groupOTU method
120
+## ##' @param object supported objects, including phylo, paml_rst,
121
+## ##'               codeml_mlc, codeml, jplace, beast, hyphy
122
+## ##' @param focus a vector of tip (label or number) or a list of tips.
123
+## ##' @param group_name name of the group, 'group' by default
124
+## ##' @param ... additional parameter
125
+## ##' @return group index
126
+## ##' @export
127
+## setGeneric("groupOTU", function(object, focus, group_name="group", ...) standardGeneric("groupOTU"))
128
+
129
+## ##' @docType methods
130
+## ##' @name groupClade
131
+## ##' @rdname groupClade-methods
132
+## ##' @title groupClade method
133
+## ##' @param object supported objects, including phylo, paml_rst,
134
+## ##'               codeml_mlc, codeml, jplace, beast, hyphy
135
+## ##' @param node a internal node or a vector of internal nodes
136
+## ##' @param group_name name of the group, 'group' by default
137
+## ##' @param ... additional parameter
138
+## ##' @return group index
139
+## ##' @export
140
+## setGeneric("groupClade", function(object, node, group_name="group", ...) standardGeneric("groupClade"))
141
+
142
+
143
+## ##' @docType methods
144
+## ##' @name scale_color
145
+## ##' @rdname scale_color-methods
146
+## ##' @title scale_color method
147
+## ##' @param object supported objects, including phylo, paml_rst,
148
+## ##'               codeml_mlc, codeml, jplace, beast, hyphy
149
+## ##' @param by one of numerical attributes
150
+## ##' @param ... additional parameter
151
+## ##' @return color vector
152
+## ##' @export
153
+## setGeneric("scale_color", function(object, by, ...) standardGeneric("scale_color"))
154 154
 
155 155
 ##' @docType methods
156 156
 ##' @name gzoom
... ...
@@ -166,17 +166,17 @@ setGeneric("scale_color", function(object, by, ...) standardGeneric("scale_color
166 166
 setGeneric("gzoom", function(object, focus, subtree=FALSE, widths=c(.3, .7), ...) standardGeneric("gzoom"))
167 167
 
168 168
 
169
-##' @docType methods
170
-##' @name drop.tip
171
-##' @rdname drop.tip-methods
172
-##' @title drop.tip method
173
-##' @param object An nhx or phylo object
174
-##' @param tip a vector of mode numeric or character specifying the tips to delete
175
-##' @param ... additional parameters
176
-##' @return updated object
177
-##' @export
178
-setGeneric (
179
-	name = "drop.tip",
180
-	def = function( object, tip, ... )
181
-		{ standardGeneric("drop.tip") }
182
-)
169
+## ##' @docType methods
170
+## ##' @name drop.tip
171
+## ##' @rdname drop.tip-methods
172
+## ##' @title drop.tip method
173
+## ##' @param object An nhx or phylo object
174
+## ##' @param tip a vector of mode numeric or character specifying the tips to delete
175
+## ##' @param ... additional parameters
176
+## ##' @return updated object
177
+## ##' @export
178
+## setGeneric (
179
+## 	name = "drop.tip",
180
+## 	def = function( object, tip, ... )
181
+## 		{ standardGeneric("drop.tip") }
182
+## )
... ...
@@ -1,95 +1,95 @@
1
-##' parse RAxML bootstrapping analysis output
2
-##'
3
-##' 
4
-##' @title read.raxml
5
-##' @param file RAxML bootstrapping analysis output
6
-##' @return raxml object
7
-##' @export
8
-##' @author Guangchuang Yu
9
-read.raxml <- function(file) {
10
-    tree.text <- readLines(file)
11
-    tree_text <- gsub('(:[0-9\\.eE+\\-]+)\\[(\\d+)\\]', '\\@\\2\\1', tree.text)
12
-    phylo <- read.tree(text=tree_text)
13
-    if(any(grepl('@', phylo$node.label))) {
14
-        bootstrap <- as.numeric(gsub("[^@]*@(\\d+)", "\\1", phylo$node.label))
15
-        phylo$node.label <- gsub("@\\d+", "", phylo$node.label)
16
-    }
1
+## ##' parse RAxML bootstrapping analysis output
2
+## ##'
3
+## ##' 
4
+## ##' @title read.raxml
5
+## ##' @param file RAxML bootstrapping analysis output
6
+## ##' @return raxml object
7
+## ##' @export
8
+## ##' @author Guangchuang Yu
9
+## read.raxml <- function(file) {
10
+##     tree.text <- readLines(file)
11
+##     tree_text <- gsub('(:[0-9\\.eE+\\-]+)\\[(\\d+)\\]', '\\@\\2\\1', tree.text)
12
+##     phylo <- read.tree(text=tree_text)
13
+##     if(any(grepl('@', phylo$node.label))) {
14
+##         bootstrap <- as.numeric(gsub("[^@]*@(\\d+)", "\\1", phylo$node.label))
15
+##         phylo$node.label <- gsub("@\\d+", "", phylo$node.label)
16
+##     }
17 17
 
18
-    if (all(phylo$node.label == "")) {
19
-        phylo$node.label <- NULL
20
-    }
18
+##     if (all(phylo$node.label == "")) {
19
+##         phylo$node.label <- NULL
20
+##     }
21 21
 
22
-    bootstrap <- data.frame(node = Ntip(phylo) + 1:phylo$Nnode,
23
-                            bootstrap = bootstrap)
22
+##     bootstrap <- data.frame(node = Ntip(phylo) + 1:phylo$Nnode,
23
+##                             bootstrap = bootstrap)
24 24
 
25
-    new("raxml",
26
-        file      = file,
27
-        fields    = "bootstrap",
28
-        treetext  = tree.text,
29
-        phylo     = phylo,
30
-        bootstrap = bootstrap
31
-        )
32
-}
25
+##     new("raxml",
26
+##         file      = file,
27
+##         fields    = "bootstrap",
28
+##         treetext  = tree.text,
29
+##         phylo     = phylo,
30
+##         bootstrap = bootstrap
31
+##         )
32
+## }
33 33
 
34 34
 
35
-##' @rdname show-methods
36
-##' @importFrom ape print.phylo
37
-##' @exportMethod show
38
-setMethod("show", signature(object = "raxml"),
39
-          function(object) {
40
-              cat("'raxml' S4 object that stored information of\n\t",
41
-                  paste0("'", object@file, "'.\n\n"))
42
-              cat("...@ tree: ")
43
-              print.phylo(get.tree(object))                  
44
-              cat("\nwith the following features available:\n")
45
-              print_fields(object)
46
-          })
35
+## ##' @rdname show-methods
36
+## ##' @importFrom ape print.phylo
37
+## ##' @exportMethod show
38
+## setMethod("show", signature(object = "raxml"),
39
+##           function(object) {
40
+##               cat("'raxml' S4 object that stored information of\n\t",
41
+##                   paste0("'", object@file, "'.\n\n"))
42
+##               cat("...@ tree: ")
43
+##               print.phylo(get.tree(object))                  
44
+##               cat("\nwith the following features available:\n")
45
+##               print_fields(object)
46
+##           })
47 47
 
48
-##' @rdname groupOTU-methods
49
-##' @exportMethod groupOTU
50
-setMethod("groupOTU", signature(object="raxml"),
51
-          function(object, focus, group_name="group") {
52
-              groupOTU_(object, focus, group_name)
53
-          }
54
-          )
48
+## ##' @rdname groupOTU-methods
49
+## ##' @exportMethod groupOTU
50
+## setMethod("groupOTU", signature(object="raxml"),
51
+##           function(object, focus, group_name="group") {
52
+##               groupOTU_(object, focus, group_name)
53
+##           }
54
+##           )
55 55
 
56
-##' @rdname groupClade-methods
57
-##' @exportMethod groupClade
58
-setMethod("groupClade", signature(object="raxml"),
59
-          function(object, node, group_name="group") {
60
-              groupClade_(object, node, group_name)
61
-          })
56
+## ##' @rdname groupClade-methods
57
+## ##' @exportMethod groupClade
58
+## setMethod("groupClade", signature(object="raxml"),
59
+##           function(object, node, group_name="group") {
60
+##               groupClade_(object, node, group_name)
61
+##           })
62 62
 
63
-##' @rdname scale_color-methods
64
-##' @exportMethod scale_color
65
-setMethod("scale_color", signature(object="raxml"),
66
-          function(object, by="bootstrap", ...) {
67
-              scale_color_(object, by, ...)
68
-          })
63
+## ##' @rdname scale_color-methods
64
+## ##' @exportMethod scale_color
65
+## setMethod("scale_color", signature(object="raxml"),
66
+##           function(object, by="bootstrap", ...) {
67
+##               scale_color_(object, by, ...)
68
+##           })
69 69
 
70 70
 
71
-##' @rdname gzoom-methods
72
-##' @exportMethod gzoom
73
-setMethod("gzoom", signature(object="raxml"),
74
-          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
75
-              gzoom.phylo(get.tree(object), focus, subtree, widths)
76
-          })
71
+## ##' @rdname gzoom-methods
72
+## ##' @exportMethod gzoom
73
+## setMethod("gzoom", signature(object="raxml"),
74
+##           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
75
+##               gzoom.phylo(get.tree(object), focus, subtree, widths)
76
+##           })
77 77
 
78 78
 
79
-##' @rdname get.tree-methods
80
-##' @exportMethod get.tree
81
-setMethod("get.tree", signature(object="raxml"),
82
-          function(object,...) {
83
-              object@phylo
84
-          }
85
-          )
79
+## ##' @rdname get.tree-methods
80
+## ##' @exportMethod get.tree
81
+## setMethod("get.tree", signature(object="raxml"),
82
+##           function(object,...) {
83
+##               object@phylo
84
+##           }
85
+##           )
86 86
 
87 87
 
88
-##' @rdname get.fields-methods
89
-##' @exportMethod get.fields
90
-setMethod("get.fields", signature(object="raxml"),
91
-          function(object, ...) {
92
-              get.fields.tree(object)
93
-          }
94
-          )
88
+## ##' @rdname get.fields-methods
89
+## ##' @exportMethod get.fields
90
+## setMethod("get.fields", signature(object="raxml"),
91
+##           function(object, ...) {
92
+##               get.fields.tree(object)
93
+##           }
94
+##           )
95 95
 
... ...
@@ -1,29 +1,29 @@
1 1
 
2
-##' @export
3
-ape::read.tree
2
+## ##' @export
3
+## ape::read.tree
4 4
 
5 5
 
6
-##' generate random tree
7
-##' @export
8
-##' @rdname rtree
9
-##' @param n number of tips in the tree
10
-##' @param rooted logcial
11
-##' @param tip.label tip label
12
-##' @param br one of the following: (i) an R function used to generate the
13
-##'           branch lengths ('rtree'; use 'NULL' to simulate only a
14
-##'           topology), or the coalescence times ('rcoal'); (ii) a
15
-##'           character to simulate a genuine coalescent tree for 'rcoal'
16
-##'           (the default); or (iii) a numeric vector for the branch
17
-##'           lengths or the coalescence times.
18
-##' @param ... additional parameters to be passed to 'br'
19
-##' @source
20
-##' This is just the imported function
21
-##' from the ape package. The documentation you should
22
-##' read for the rtree function can be found here: \link[ape]{rtree}
23
-##'
24
-##' @seealso
25
-##' \link[ape]{rtree}
26
-rtree <- ape::rtree
6
+## ##' generate random tree
7