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guangchuang yu
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as.data.frame & fortify method for treedata
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‎.Rbuildignore

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^.*\.Rproj$
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^\.Rproj\.user$
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Makefile

‎.gitignore

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.Rproj.user
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.Rhistory
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.RData
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*~

‎DESCRIPTION

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Package: tidytree
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Title: What the Package Does (one line, title case)
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Version: 0.0.1
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Authors@R: person("First", "Last", email = "[email protected]", role = c("aut", "cre"))
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Description: What the package does (one paragraph).
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Depends:
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R (>= 3.3.2)
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Imports:
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ape,
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ggplot2,
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magrittr,
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methods,
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treeio
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Suggests:
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knitr,
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prettydoc
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VignetteBuilder: knitr
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ByteCompile: true
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License: Artistic-2.0
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URL: https://guangchuangyu.github.io/tidytree
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BugReports: https://github.com/GuangchuangYu/tidytree/issues
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Encoding: UTF-8
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LazyData: true
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RoxygenNote: 5.0.1

‎Makefile

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PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
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PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
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PKGSRC := $(shell basename `pwd`)
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all: rd check clean
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rd:
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Rscript -e 'roxygen2::roxygenise(".")'
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build:
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cd ..;\
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R CMD build $(PKGSRC)
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build2:
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cd ..;\
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R CMD build --no-build-vignettes $(PKGSRC)
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install:
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cd ..;\
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R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
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check: build
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cd ..;\
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Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
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check2: build
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cd ..;\
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R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
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bioccheck:
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cd ..;\
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Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
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clean:
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cd ..;\
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$(RM) -r $(PKGNAME).Rcheck/
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‎NAMESPACE

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# Generated by roxygen2: do not edit by hand
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S3method(as.data.frame,phylo)
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S3method(as.data.frame,treedata)
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S3method(fortify,phylo)
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S3method(fortify,treedata)
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export("%>%")
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export(get.offspring.tip)
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export(get.path)
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export(getNodeNum)
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export(getRoot)
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export(is.ggtree)
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export(nodeid)
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importFrom(ape,extract.clade)
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importFrom(ape,reorder.phylo)
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importFrom(ggplot2,fortify)
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importFrom(magrittr,"%>%")
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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,slot)
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importFrom(treeio,Nnode)
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importFrom(treeio,Ntip)
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importFrom(treeio,get.tree)

‎NEWS

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CHANGES IN VERSION 0.0.1
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------------------------
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o as.data.frame & fortify method for treedata object <2016-12-06, Tue>

‎R/as-data-frame.R

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##' @method as.data.frame treedata
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##' @export
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##' @importFrom treeio Nnode
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##' @importFrom treeio Ntip
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as.data.frame.treedata <- function(x, row.names, optional, branch.length = "branch.length", ...) {
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tree <- set_branch_length(x, branch.length)
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res <- as.data.frame(tree@phylo)
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tree_anno <- get_tree_data(x)
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if (nrow(tree_anno) > 0) {
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res <- merge(res, tree_anno, by="node", all.x=TRUE)
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}
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return(res)
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}
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##' @method as.data.frame phylo
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##' @export
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as.data.frame.phylo <- function(x, row.names, optional, branch.length = "branch.length", ...) {
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phylo <- x
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ntip <- Ntip(phylo)
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N <- Nnode(phylo, internal.only=FALSE)
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tip.label <- phylo[["tip.label"]]
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res <- as.data.frame(phylo[["edge"]])
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colnames(res) <- c("parent", "node")
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if (!is.null(phylo$edge.length))
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res$branch.length <- phylo$edge.length
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label <- rep(NA, N)
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label[1:ntip] <- tip.label
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if ( !is.null(phylo$node.label) ) {
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label[(ntip+1):N] <- phylo$node.label
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}
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label.df <- data.frame(node=1:N, label=label)
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res <- merge(res, label.df, by='node', all.y=TRUE)
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isTip <- rep(FALSE, N)
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isTip[1:ntip] <- TRUE
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res$isTip <- isTip
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return(res)
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}
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‎R/fortify.R

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##' @importFrom ggplot2 fortify
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##' @method fortify phylo
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##' @export
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fortify.phylo <- function(model, data, layout="rectangular", branch.length ="branch.length",
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ladderize=TRUE, right=FALSE, mrsd=NULL, ...) {
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model <- set_branch_length(model, branch.length)
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x <- reorder.phylo(get.tree(model), "postorder")
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if (is.null(x$edge.length) || branch.length == "none") {
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xpos <- getXcoord_no_length(x)
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} else {
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xpos <- getXcoord(x)
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}
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ypos <- getYcoord(x)
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N <- Nnode(x, internal.only=FALSE)
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xypos <- data.frame(node=1:N, x=xpos, y=ypos)
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df <- as.data.frame(model, branch.length="branch.length") # already set by set_branch_length
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idx <- is.na(df$parent)
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df$parent[idx] <- df$node[idx]
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rownames(df) <- df$node
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res <- merge(df, xypos, by='node', all.y=TRUE)
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## add branch mid position
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res <- calculate_branch_mid(res)
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## ## angle for all layout, if 'rectangular', user use coord_polar, can still use angle
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res <- calculate_angle(res)
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res
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}
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##' @method fortify treedata
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##' @export
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fortify.treedata <- fortify.phylo
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calculate_angle <- function(data) {
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data$angle <- 360/(diff(range(data$y)) + 1) * data$y
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return(data)
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}

‎R/reexports.R

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##' @importFrom magrittr %>%
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##' @export
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magrittr::`%>%`
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