git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@121115 bc3139a8-67e5-0310-9ffc-ced21a209358
Guangchuang Yu authored on 19/09/2016 07:21:18
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Package: ggtree |
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Type: Package |
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Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data |
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-Version: 1.5.13 |
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+Version: 1.5.14 |
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Author: Guangchuang Yu and Tommy Tsan-Yuk Lam |
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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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@@ -35,6 +35,7 @@ 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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+export(as.polytomy) |
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| 38 | 39 |
export(collapse) |
| 39 | 40 |
export(decimal2Date) |
| 40 | 41 |
export(download.phylopic) |
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@@ -152,6 +153,7 @@ exportMethods(scale_color) |
| 152 | 153 |
exportMethods(show) |
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importFrom(ape,Nnode) |
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importFrom(ape,Ntip) |
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+importFrom(ape,di2multi) |
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| 155 | 157 |
importFrom(ape,drop.tip) |
| 156 | 158 |
importFrom(ape,extract.clade) |
| 157 | 159 |
importFrom(ape,getMRCA) |
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@@ -1,3 +1,10 @@ |
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+CHANGES IN VERSION 1.5.14 |
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+------------------------ |
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+ o update angle calculation for geom_tiplab <2016-09-13, Thu> |
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+ o as.polytomy to collapse binary tree to polytomy by applying 'fun' to selected 'feature' (e.g. bootstrap value less than 70). <2016-09-13, Tue> |
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+ + currently only phylo object supported. |
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+ + add test for as.polytomy |
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+ |
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CHANGES IN VERSION 1.5.13 |
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------------------------ |
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o facet_plot for plotting data with tree <2016-09-06, Tue> |
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new file mode 100644 |
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@@ -0,0 +1,43 @@ |
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+ |
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+##' collapse binary tree to polytomy by applying 'fun' to 'feature' |
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+##' |
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+##' |
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+##' @title as.polytomy |
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+##' @param tree tree object |
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+##' @param feature selected feature |
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+##' @param fun function to select nodes to collapse |
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+##' @return polytomy tree |
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+##' @author Guangchuang |
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+##' @importFrom ape Ntip |
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+##' @importFrom ape di2multi |
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+##' @export |
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+as.polytomy <- function(tree, feature, fun) {
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+ if (!is(tree, 'phylo')) {
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+ stop("currently only 'phylo' object is supported...")
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+ } |
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+ |
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+ df <- fortify(tree) |
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+ phylo <- get.tree(tree) |
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+ |
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+ if (feature == 'node.label') {
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+ feat <- df[!df$isTip, 'label'] |
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+ } else if (feature == 'tip.label') {
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+ feat <- df[df$isTip, 'label'] |
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+ } else {
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+ feat <- df[, feature] |
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+ } |
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+ |
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+ idx <- which(fun(feat)) |
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+ if (feature == 'node.label') {
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+ nodes <- Ntip(phylo) + df$node[idx] |
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+ } else {
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+ nodes <- df$node[idx] |
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+ } |
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+ edge_idx <- match(nodes, phylo$edge[,2]) |
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+ phylo$edge.length[edge_idx] <- 0 |
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+ poly_tree <- di2multi(phylo) |
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+ ## |
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+ ## map stats to poly_tree and update tree object |
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+ ## |
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+ return(poly_tree) |
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+} |
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@@ -557,16 +557,16 @@ as.data.frame.phylo_ <- function(x, layout="rectangular", |
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## add branch mid position |
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res <- calculate_branch_mid(res) |
| 559 | 559 |
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- ## angle for all layout, if 'rectangular', user use coord_polar, can still use angle |
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- ## if (layout == "circular") {
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- idx <- match(1:N, order(res$y)) |
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- ## angle <- -360/(3+N) * (1:N+1) |
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- angle <- 360/(3+N) * (1:N+1) |
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- angle <- angle[idx] |
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- ## res$angle <- angle + 90 |
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- res$angle <- angle |
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+ ## ## angle for all layout, if 'rectangular', user use coord_polar, can still use angle |
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+ ## ## if (layout == "circular") {
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+ ## idx <- match(1:N, order(res$y)) |
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+ ## ## angle <- -360/(3+N) * (1:N+1) |
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+ ## angle <- 360/(3+N) * (1:N+1) |
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+ ## angle <- angle[idx] |
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+ ## ## res$angle <- angle + 90 |
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+ ## res$angle <- angle |
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## } |
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- |
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+ res$angle <- 360/(diff(range(res$y)) + 1) * res$y |
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return(res) |
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} |
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@@ -100,7 +100,7 @@ |
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##' @author Guangchuang Yu |
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`%+>%` <- function(p, data) {
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df <- p$data |
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- res <- merge(df[, c('label', 'y')], data, by.x='label', by.y=1, all.x=TRUE)
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+ res <- merge(df[, c('label', 'y')], data, by.x='label', by.y=1) ## , all.x=TRUE)
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| 104 | 104 |
lv <- levels(df$panel) |
| 105 | 105 |
res$panel <- factor(lv[length(lv)], levels=lv) |
| 106 | 106 |
return(res) |
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@@ -1,9 +1,9 @@ |
| 1 | 1 |
ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data |
| 2 | 2 |
=========================================================================================================================== |
| 3 | 3 |
|
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-[](https://bioconductor.org/packages/ggtree) [](https://github.com/GuangchuangYu/ggtree) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
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+[](https://bioconductor.org/packages/ggtree) [](https://github.com/GuangchuangYu/ggtree) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
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| 5 | 5 |
|
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-[](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ggtree) [](https://github.com/GuangchuangYu/ggtree/commits/master) [](https://github.com/GuangchuangYu/ggtree/network) [](https://github.com/GuangchuangYu/ggtree/stargazers) [](https://awesome-r.com/#awesome-r-graphic-displays) |
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+[](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ggtree) [](https://github.com/GuangchuangYu/ggtree/commits/master) [](https://github.com/GuangchuangYu/ggtree/network) [](https://github.com/GuangchuangYu/ggtree/stargazers) [](https://awesome-r.com/#awesome-r-graphic-displays) |
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[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [](https://travis-ci.org/GuangchuangYu/ggtree) [](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html) |
| 9 | 9 |
|
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@@ -17,7 +17,7 @@ Please cite the following article when using `ggtree`: |
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**G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. *accepted* |
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-[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://www.altmetric.com/details/10533079) |
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+[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://www.altmetric.com/details/10533079) |
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| 21 | 21 |
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------------------------------------------------------------------------ |
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|
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@@ -30,7 +30,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/ |
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### Download stats |
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-[](https://bioconductor.org/packages/stats/bioc/ggtree/) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
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+[](https://bioconductor.org/packages/stats/bioc/ggtree/) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
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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/as.polytomy.R |
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+\name{as.polytomy}
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+\alias{as.polytomy}
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+\title{as.polytomy}
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+\usage{
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+as.polytomy(tree, feature, fun) |
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+} |
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+\arguments{
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+\item{tree}{tree object}
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+ |
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+\item{feature}{selected feature}
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+ |
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+\item{fun}{function to select nodes to collapse}
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+} |
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+\value{
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+polytomy tree |
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+} |
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+\description{
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+collapse binary tree to polytomy by applying 'fun' to 'feature' |
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+} |
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+\author{
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+Guangchuang |
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+} |
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+ |
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new file mode 100644 |
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+context('as.polytomy')
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+ |
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+test_that('collapse tree to polytomy', {
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+ file <- system.file("extdata/RAxML", "RAxML_bipartitions.H3", package="ggtree")
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+ tree <- read.tree(file) |
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+ cutoff <- 70 |
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+ tree2 <- as.polytomy(tree, 'node.label', function(x) as.numeric(x) < cutoff) |
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+ expect_true(all(as.numeric(tree2$node.label) > 70, na.rm=T)) |
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+}) |
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+ |