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CHANGES IN VERSION 1.5.16 |
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------------------------ |
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+ o read.phyloT for parsing newick format of phyloT output <2016-10-11, Tue> |
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+ + https://www.biostars.org/p/210401/#216128 |
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o fixed aes mapping in geom_strip <2016-10-11, Tue> |
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o fixed R check <2016-10-10, Mon> |
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+ check.aes parameter is not available in release version of ggplot2 yet |
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new file mode 100644 |
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+##' parse output from phyloT |
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+##' |
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+##' |
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+##' @title read.phyloT |
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+##' @param file newick tree file |
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+##' @param ... additional parameters to read.tree |
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+##' @return phylo object |
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+##' @references \url{http://phylot.biobyte.de/}
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+##' @export |
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+##' @author guangchuang yu |
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+read.phyloT <- function(file, ...) {
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+ x <- readLines(file) |
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+ x <- paste0(gsub("\\s+", "", x), collapse="")
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+ x <- sub("^\\(", "", x) %>% sub("\\);", ";", .)
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+ res <- tryCatch(read.tree(text=x, ...), error=function(e) NULL) |
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+ if (is.null(res)) {
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+ msg <- paste("`read.phyloT` only supports newick format with setting of",
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+ "`Internal nodes` to `collapsed`, and `Polytomy` to `No`.", |
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+ "\nURL: http://phylot.biobyte.de/") |
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+ stop(msg) |
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+ } |
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+ return(res) |
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+} |
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+ |
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new file mode 100644 |
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/phyloT.R |
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+\name{read.phyloT}
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+\alias{read.phyloT}
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+\title{read.phyloT}
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+\usage{
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+read.phyloT(file, ...) |
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+} |
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+\arguments{
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+\item{file}{newick tree file}
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+ |
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+\item{...}{additional parameters to read.tree}
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+} |
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+\value{
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+phylo object |
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+} |
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+\description{
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+parse output from phyloT |
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+} |
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+\author{
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+guangchuang yu |
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+} |
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+\references{
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+\url{http://phylot.biobyte.de/}
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+} |
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+ |
