1. ggtree
  2. Commit 5c02803ef763506dacd166014c4a2463c1132820
Browse code

revts

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@123745 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 07/11/2016 03:17:14
Showing 7 changed files
DESCRIPTION
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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: 1.7.2
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+Version: 1.7.3
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 Authors@R: c(
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 	   person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph")),
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 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = c("aut", "ths")),
NAMESPACE
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@@ -111,6 +111,7 @@ export(read.raxml)
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 export(read.tree)
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 export(reroot)
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 export(rescale_tree)
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+export(revts)
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 export(rotate)
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 export(rotate_tree)
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 export(rtree)
NEWS
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+CHANGES IN VERSION 1.7.3
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+------------------------
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+ o reverse timescale x-axis <2016-11-07, Mon>
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+   + https://github.com/GuangchuangYu/ggtree/issues/87
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+
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 CHANGES IN VERSION 1.7.2
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 ------------------------
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+ o make missing colors in gheatmap invisible (previously use 'white') <2016-11-03, Thu>
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  o xlim_expand for setting x axis limits of specific panel <2016-11-01, Tue>
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    + xlim_tree is now a specific case of xlim_expand(xlim, panel='Tree')
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  o bug fixed of parsing tree text in beast file <2016-10-31, Mon>
R/gheatmap.R
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@@ -79,9 +79,9 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=
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         p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), width=width, color=color, inherit.aes=FALSE)
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     }
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     if (is(dd$value,"numeric")) {
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-        p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value="white")
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+        p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value=NA) # "white")
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     } else {
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-        p2 <- p2 + scale_fill_discrete(na.value="white")
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+        p2 <- p2 + scale_fill_discrete(na.value=NA) #"white")
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     }
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     if (colnames) {
R/xlim.R
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@@ -26,3 +26,17 @@ xlim_expand <- function(xlim, panel) {
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     geom_blank(aes_(x=~x), dummy, inherit.aes = FALSE)
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 }
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+##' reverse timescle x-axis
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+##'
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+##'
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+##' @title revts
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+##' @param treeview treeview
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+##' @return updated treeview
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+##' @export
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+##' @author guangchuang yu
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+revts <- function(treeview) {
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+    x <- treeview$data$x
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+    x <- x - max(x)
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+    treeview$data$x <- x
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+    treeview
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+}
README.md
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 ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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 ===========================================================================================================================
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.1-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.2-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-15734/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.2-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.2-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-16279/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)
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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--01-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--07-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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 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
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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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-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-275-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-274-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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 ------------------------------------------------------------------------
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 ### Download stats
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-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-15734/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-16279/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)
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-         +-------------------------+------------------------+-------------------------+----------------+
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+         +------------------------+-----------------------+-----------------------+--------------------+
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+         |                                                                                    *        |
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          |                                                                                         *   |
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     1500 +                                                                                             +
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     1000 +                                                                                             +
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-     500 +                                 *                                                           +
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+     500 +                                *                                                            +
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-         |                    *   *    *                                                               |
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+         |                   *   *   *                                                                 |
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-         |                *                                                                            |
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+         |               *                                                                             |
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          |                                                                                             |
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-       0 +   *   *    *                                                                                +
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-         +-------------------------+------------------------+-------------------------+----------------+
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-       2015                     2015.5                    2016                     2016.5
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+       0 +   *   *   *                                                                                 +
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+         +------------------------+-----------------------+-----------------------+--------------------+
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+       2015                    2015.5                   2016                   2016.5
man/revts.Rd
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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/xlim.R
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+\name{revts}
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+\alias{revts}
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+\title{revts}
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+\usage{
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+revts(treeview)
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+}
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+\arguments{
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+\item{treeview}{treeview}
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+}
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+\value{
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+updated treeview
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+}
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+\description{
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+reverse timescle x-axis
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+}
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+\author{
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+guangchuang yu
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+}
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+