git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122189 bc3139a8-67e5-0310-9ffc-ced21a209358
Guangchuang Yu authored on 11/10/2016 10:03:03
| ... | ... |
@@ -1,5 +1,7 @@ |
| 1 | 1 |
CHANGES IN VERSION 1.5.16 |
| 2 | 2 |
------------------------ |
| 3 |
+ o read.phyloT for parsing newick format of phyloT output <2016-10-11, Tue> |
|
| 4 |
+ + https://www.biostars.org/p/210401/#216128 |
|
| 3 | 5 |
o fixed aes mapping in geom_strip <2016-10-11, Tue> |
| 4 | 6 |
o fixed R check <2016-10-10, Mon> |
| 5 | 7 |
+ check.aes parameter is not available in release version of ggplot2 yet |
| 6 | 8 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,24 @@ |
| 1 |
+##' parse output from phyloT |
|
| 2 |
+##' |
|
| 3 |
+##' |
|
| 4 |
+##' @title read.phyloT |
|
| 5 |
+##' @param file newick tree file |
|
| 6 |
+##' @param ... additional parameters to read.tree |
|
| 7 |
+##' @return phylo object |
|
| 8 |
+##' @references \url{http://phylot.biobyte.de/}
|
|
| 9 |
+##' @export |
|
| 10 |
+##' @author guangchuang yu |
|
| 11 |
+read.phyloT <- function(file, ...) {
|
|
| 12 |
+ x <- readLines(file) |
|
| 13 |
+ x <- paste0(gsub("\\s+", "", x), collapse="")
|
|
| 14 |
+ x <- sub("^\\(", "", x) %>% sub("\\);", ";", .)
|
|
| 15 |
+ res <- tryCatch(read.tree(text=x, ...), error=function(e) NULL) |
|
| 16 |
+ if (is.null(res)) {
|
|
| 17 |
+ msg <- paste("`read.phyloT` only supports newick format with setting of",
|
|
| 18 |
+ "`Internal nodes` to `collapsed`, and `Polytomy` to `No`.", |
|
| 19 |
+ "\nURL: http://phylot.biobyte.de/") |
|
| 20 |
+ stop(msg) |
|
| 21 |
+ } |
|
| 22 |
+ return(res) |
|
| 23 |
+} |
|
| 24 |
+ |
| 0 | 25 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,26 @@ |
| 1 |
+% Generated by roxygen2: do not edit by hand |
|
| 2 |
+% Please edit documentation in R/phyloT.R |
|
| 3 |
+\name{read.phyloT}
|
|
| 4 |
+\alias{read.phyloT}
|
|
| 5 |
+\title{read.phyloT}
|
|
| 6 |
+\usage{
|
|
| 7 |
+read.phyloT(file, ...) |
|
| 8 |
+} |
|
| 9 |
+\arguments{
|
|
| 10 |
+\item{file}{newick tree file}
|
|
| 11 |
+ |
|
| 12 |
+\item{...}{additional parameters to read.tree}
|
|
| 13 |
+} |
|
| 14 |
+\value{
|
|
| 15 |
+phylo object |
|
| 16 |
+} |
|
| 17 |
+\description{
|
|
| 18 |
+parse output from phyloT |
|
| 19 |
+} |
|
| 20 |
+\author{
|
|
| 21 |
+guangchuang yu |
|
| 22 |
+} |
|
| 23 |
+\references{
|
|
| 24 |
+\url{http://phylot.biobyte.de/}
|
|
| 25 |
+} |
|
| 26 |
+ |