1. ggtree
  2. Commit 177144870a47dfb6dd89f4f4e607df1bcb89d9a3
Browse code

bug fixed in geom_treescale

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120154 bc3139a8-67e5-0310-9ffc-ced21a209358

g.yu authored on 16/08/2016 04:18:17
Showing 4 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: 1.5.9
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+Version: 1.5.10
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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.
NEWS
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@@ -1,3 +1,8 @@
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+CHANGES IN VERSION 1.5.10
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+------------------------
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+ o fixed issue #72 for label of geom_treescale not displayed <2016-08-16, Tue>
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+   + https://github.com/GuangchuangYu/ggtree/issues/72
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+
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 CHANGES IN VERSION 1.5.9
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 ------------------------
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  o update citation info <2016-08-12, Fri>
R/geom_treescale.R
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@@ -19,7 +19,7 @@ geom_treescale <- function(x=NULL, y=NULL, width=NULL, offset=NULL, color="black
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     data=NULL
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     position="identity"
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     show.legend=NA
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-    na.rm=FALSE
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+    na.rm=TRUE
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     inherit.aes=FALSE
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     default_aes <- aes_(x=~x, y=~y)
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@@ -74,7 +74,7 @@ stat_treeScaleText <- function(mapping=NULL, data=NULL,
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                                xx, yy, width, offset, color, ...,
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                                show.legend=NA, inherit.aes=TRUE, na.rm=FALSE) {
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-    default_aes <- aes_(x=~x, y=~y, label=~label)
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+    default_aes <- aes_(x=~x, y=~y, label=~x)
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     if (is.null(mapping)) {
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         mapping <- default_aes
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     } else {
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@@ -149,9 +149,9 @@ get_treescale_position <- function(data, xx, yy, width, offset=NULL) {
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          TextPosition=data.frame(x=x+d/2, y=y+offset, label=d))
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 }
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-##' add evolution distance legend
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-##'
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-##'
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+## ##' add evolution distance legend
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+## ##'
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+## ##'
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 ## ##' @title add_legend
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 ## ##' @param p tree view
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 ## ##' @param width width of legend
README.md
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@@ -3,9 +3,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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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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-[![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--08--12-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![commit](http://www.bioconductor.org/shields/commits/bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source) [![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)
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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--08--16-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![commit](http://www.bioconductor.org/shields/commits/bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source) [![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)
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.14-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.9-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) [![post](http://www.bioconductor.org/shields/posts/ggtree.svg)](https://support.bioconductor.org/t/ggtree/) [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/)
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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.16-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.10-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) [![post](http://www.bioconductor.org/shields/posts/ggtree.svg)](https://support.bioconductor.org/t/ggtree/) [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/)
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 The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.
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@@ -28,7 +28,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
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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-11940/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![month](https://img.shields.io/badge/downloads-1091/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-12041/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![month](https://img.shields.io/badge/downloads-1091/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree/)
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          +---------------------------+---------------------------+----------------------------+--------+
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