1. ggtree
  2. Commit b14d75e3013c067ae2fc4f89f05bacc80a0645c0
Browse code

postorder

guangchuang yu authored on 28/11/2016 05:42:43
Showing 3 changed files
NEWS
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@@ -1,5 +1,6 @@
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 CHANGES IN VERSION 1.7.4
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 ------------------------
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+ o reorder phylo to postorder before ladderrize <2016-11-28, Mon>
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  o allow yscale to use data stored in phylo4d object <2016-11-24, Thu>
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    + https://github.com/GuangchuangYu/ggtree/issues/98
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  o groupOTU method now accept 'overlap = c("overwrite", "origin", "abandon")' parameter <2016-11-16, Wed>
R/method-fortify.R
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@@ -439,16 +439,17 @@ as.phylo.phylo4 <- function(phylo4) {
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 ##' @param ... additional parameter
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 ##' @return data.frame
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 ##' @importFrom ape ladderize
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+##' @importFrom ape reorder.phylo
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 ##' @importFrom ggplot2 fortify
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 ##' @method fortify phylo
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 ##' @export
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 ##' @author Yu Guangchuang
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 fortify.phylo <- function(model, data, layout="rectangular",
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                           ladderize=TRUE, right=FALSE, mrsd=NULL, as.Date=FALSE, ...) {
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+    tree <- reorder.phylo(model, 'postorder')
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+
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     if (ladderize == TRUE) {
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-        tree <- ladderize(model, right=right)
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-    } else {
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-        tree <- model
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+        tree <- ladderize(tree, right=right)
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     }
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     if (! is.null(tree$edge.length)) {
README.md
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@@ -4,7 +4,7 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 [![releaseVersion](https://img.shields.io/badge/release%20version-1.6.4-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.4-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-16878/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1621/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />
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-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--11--24-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--11--28-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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