Browse code

bioc git transition

guangchuang yu authored on 18/07/2017 08:10:02
Showing100 changed files

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@@ -43,4 +43,4 @@ BugReports: https://github.com/GuangchuangYu/ggtree/issues
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 Packaged: 2014-12-03 08:16:14 UTC; root
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 biocViews: Alignment, Annotation, Clustering, DataImport,
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     MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization
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-RoxygenNote: 6.0.1
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+RoxygenNote: 5.0.1
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@@ -71,7 +71,16 @@ svncommit:
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 	git checkout master;\
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 	git merge devel
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+
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 gitmaintain:
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 	git gc --auto;\
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 	git prune -v;\
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 	git fsck --full
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+
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+push:
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+	git push -u origin master;\
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+	git checkout bioc;\
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+	git merge master;\
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+	git push upstream master;\
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+	git checkout master
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+
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@@ -14,7 +14,6 @@ html_preview: false
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 library("txtplot")
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 library("badger")
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 library("ypages")
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-library("ggalt")
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 library("ggplot2")
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 ```
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@@ -43,6 +42,7 @@ library("ggplot2")
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 [![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)
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+
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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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 [![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ggtree.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)
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@@ -78,7 +78,9 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali
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 ```{r echo=F, comment=NA}
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 d <- get_article_cite_history('DO5oG40AAAAJ', 'HtEfBTGE9r8C')
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 ## txtplot(d$year, d$cites)
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-p <- ggplot(d, aes(year, cites)) + geom_lollipop(point.size=3, point.colour='firebrick') +
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+## library("ggalt")
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+## p <- ggplot(d, aes(year, cites)) + geom_lollipop(point.size=3, point.colour='firebrick') +
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+p <- ggplot(d, aes(year, cites)) + geom_segment(aes(xend=year, yend=0)) + geom_point(size=3, color='firebrick') +
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     theme_minimal() + xlab(NULL) + ylab(NULL) + labs(title="Citation", caption="data from Google Scholar")
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 ggsave(p, file="docs/citation.png", width=8, height=4)
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 ```
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@@ -94,6 +96,7 @@ ggsave(p, file="docs/citation.png", width=8, height=4)
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 `r badge_bioc_download("ggtree", "month", "blue")`
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+
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 ```{r echo=F, message=F, comment=NA}
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 x <- dlstats::bioc_stats("ggtree")
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 x <- x[-nrow(x), ] # last month data is not complete
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@@ -136,3 +139,4 @@ Support this project by becoming a sponsor. Your logo will show up here with a l
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+
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@@ -2,11 +2,14 @@
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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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+    ## Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
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+    ## Please reinstall dplyr to avoid random crashes or undefined behavior.
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+
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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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 [![](https://img.shields.io/badge/release%20version-1.8.1-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.9.2-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) [![](https://img.shields.io/badge/download-17163/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-885/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-2017--07--17-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-2017--07--18-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) [![Backers on Open Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers) [![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)
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@@ -18,3 +18,4 @@ convert Date to decimal format, eg "2014-05-05" to "2014.34"
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -17,3 +17,4 @@ list of all child node id's from starting node.
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 \description{
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 Get all children of node from df tree using breath-first.
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 }
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+
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@@ -18,3 +18,4 @@ named list of subtrees with the root id of subtree and list of node id's making
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 Get all subtrees of specified node. This includes all ancestors and relatives of node and
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 return named list of subtrees.
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 }
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+
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@@ -20,3 +20,4 @@ Find Most Recent Common Ancestor among a vector of tips
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -31,3 +31,4 @@ print(tree)
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 \author{
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 ygc
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 }
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+
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@@ -30,3 +30,4 @@ p \%<+\% dd + geom_text(aes(color=place, label=label), hjust=-0.5)
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 \author{
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 Yu Guangchuang
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 }
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+
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@@ -20,3 +20,4 @@ update data with tree info (y coordination and panel)
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -29,3 +29,4 @@ add colorbar legend
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -31,3 +31,4 @@ annotation taxa with images
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -20,3 +20,4 @@ merge phylo and output of boot.phylo to 'apeBootstrap' object
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -18,3 +18,4 @@ list with tree data.frame with updated layout using daylight algorithm and max_c
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 Apply the daylight alorithm to adjust the spacing between the subtrees and tips of the
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 specified node.
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 }
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+
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@@ -30,3 +30,4 @@ is.binary.tree(tr2)
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 \author{
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 Guangchuang Yu \url{http://ygc.name}
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 }
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+
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@@ -27,3 +27,4 @@ convert phylo to data.frame
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 \author{
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 Yu Guangchuang
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 }
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+
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@@ -22,3 +22,4 @@ collapse binary tree to polytomy by applying 'fun' to 'feature'
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 \author{
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 Guangchuang
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 }
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+
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@@ -17,9 +17,10 @@ tree view
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 \description{
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 collapse a clade
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 }
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-\seealso{
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-expand
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-}
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 \author{
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 Guangchuang Yu
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 }
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+\seealso{
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+expand
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+}
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+
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@@ -18,3 +18,4 @@ convert decimal format to Date, eg "2014.34" to "2014-05-05"
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -21,3 +21,4 @@ capture name of variable
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 x <- 1
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 eval(.(x)[[1]])
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 }
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+
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@@ -24,3 +24,4 @@ download phylopic
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -17,9 +17,10 @@ tree view
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 \description{
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 expand collased clade
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 }
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-\seealso{
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-collapse
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-}
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 \author{
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 Guangchuang Yu
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 }
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+\seealso{
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+collapse
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+}
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+
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@@ -28,3 +28,4 @@ plot tree associated data in an additional panel
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -22,3 +22,4 @@ flip position of two selected branches
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -33,3 +33,4 @@ fortify a phylo to data.frame
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 \author{
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 Yu Guangchuang
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 }
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+
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@@ -24,3 +24,4 @@ add horizontal align lines
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 \author{
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 Yu Guangchuang
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 }
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+
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@@ -30,10 +30,11 @@ highlights the two direct descendant clades of an internal node
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 Particularly useful when studying neighboring clades. Note that balances that
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 correspond to multichotomies will not be displayed.
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 }
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+\author{
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+Justin Silverman
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+}
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 \references{
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 J. Silverman, et al. \emph{A phylogenetic transform enhances
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   analysis of compositional microbiota data}. (in preparation)
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 }
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-\author{
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-Justin Silverman
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-}
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+
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@@ -48,3 +48,4 @@ annotate a clade with bar and text label
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -27,3 +27,4 @@ layer of hilight clade with rectangle
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -45,9 +45,10 @@ label layer
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 \description{
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 geom_label2 support aes(subset) via setup_data
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 }
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-\seealso{
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-\link[ggplot2]{geom_label}
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-}
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 \author{
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 Guangchuang Yu
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 }
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+\seealso{
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+\link[ggplot2]{geom_label}
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+}
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+
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@@ -31,3 +31,4 @@ add node point
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 \author{
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 Guangchuang Yu
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 }
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@@ -28,9 +28,10 @@ point layer
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 \description{
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 geom_point2 support aes(subset) via setup_data
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 }
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-\seealso{
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-\link[ggplot2]{geom_point}
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-}
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 \author{
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 Guangchuang Yu
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 }
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+\seealso{
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+\link[ggplot2]{geom_point}
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+}
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+
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@@ -20,3 +20,4 @@ bar of range (HPD, range etc) to present uncertainty of evolutionary inference
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 \author{
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 Guangchuang Yu
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 }
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@@ -31,3 +31,4 @@ add root point
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 \author{
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 Guangchuang Yu
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 }
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@@ -33,9 +33,10 @@ add segment layer
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 \description{
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 geom_segment2 support aes(subset) via setup_data
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 }
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-\seealso{
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-\link[ggplot2]{geom_segment}
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-}
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 \author{
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 Guangchuang Yu
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 }
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+\seealso{
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+\link[ggplot2]{geom_segment}
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+}
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+
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@@ -51,3 +51,4 @@ annotate associated taxa (from taxa1 to taxa2, can be Monophyletic, Polyphyletic
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -26,3 +26,4 @@ link between taxa
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -40,9 +40,10 @@ text layer
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 \description{
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 geom_text2 support aes(subset) via setup_data
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 }
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-\seealso{
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-\link[ggplot2]{geom_text}
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-}
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 \author{
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 Guangchuang Yu
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 }
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+\seealso{
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+\link[ggplot2]{geom_text}
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+}
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+
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@@ -38,3 +38,4 @@ ggtree(tr) + geom_tiplab()
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 \author{
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 Yu Guangchuang
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 }
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+
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@@ -19,9 +19,10 @@ tip label layer
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 \description{
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 add tip label for circular layout
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 }
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-\references{
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-\url{https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0}
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-}
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 \author{
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 Guangchuang Yu
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 }
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+\references{
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+\url{https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0}
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+}
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+
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@@ -31,3 +31,4 @@ add tip point
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -27,3 +27,4 @@ add tree layer
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 \author{
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 Yu Guangchuang
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 }
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+
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@@ -20,3 +20,4 @@ add tree layer
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 \author{
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 Yu Guangchuang
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 }
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+
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@@ -33,3 +33,4 @@ add tree scale
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -20,3 +20,4 @@ extract offspring tips
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 \author{
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 ygc
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 }
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+
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@@ -22,3 +22,4 @@ path from start node to end node
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -24,3 +24,4 @@ download phylopic and convert to grob object
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -17,3 +17,4 @@ list of child node ids of parent
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 \description{
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 Get list of child node id numbers of parent node
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 }
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+
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@@ -19,3 +19,4 @@ angle in range [-1, 1], i.e. degrees/180, radians/pi
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 \description{
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 Get the angle between the two nodes specified.
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 }
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+
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@@ -15,3 +15,4 @@ list of node id's in breadth-first order.
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 \description{
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 Get the nodes of tree from root in breadth-first order.
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 }
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+
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@@ -17,3 +17,4 @@ integer node id of parent
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 \description{
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 Get parent node id of child node.
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 }
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+
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@@ -17,3 +17,4 @@ list of all child node id's from starting node.
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 \description{
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 Get all children of node from tree, including start_node.
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 }
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+
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@@ -18,3 +18,4 @@ named list of subtrees with the root id of subtree and list of node id's making
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 Get all subtrees of node, as well as remaining branches of parent (ie, rest of tree structure as subtree)
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 return named list of subtrees with list name as starting node id.
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 }
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+
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@@ -20,3 +20,4 @@ named list with right and left angles in range [0,2] i.e 1 = 180 degrees, 1.5 =
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 Find the right (clockwise rotation, angle from +ve x-axis to furthest subtree nodes) and
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 left (anti-clockwise angle from +ve x-axis to subtree)
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 }
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+
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@@ -22,3 +22,4 @@ get position of balance (xmin, xmax, ymin, ymax)
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 \author{
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 Justin Silverman
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 }
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+
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@@ -20,3 +20,4 @@ get position of clade (xmin, xmax, ymin, ymax)
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -21,3 +21,4 @@ for labeling column names of heatmap produced by `gheatmap` function
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -20,3 +20,4 @@ get taxa name of a selected node (or tree if node=NULL) sorted by their position
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -11,3 +11,4 @@ StatBalance
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 StatHilight
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 }
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 \keyword{datasets}
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+
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@@ -3,9 +3,8 @@
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 \docType{package}
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 \name{ggtree}
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 \alias{ggtree}
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-\alias{package-ggtree}
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 \alias{ggtree-package}
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-\alias{ggtree}
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+\alias{package-ggtree}
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 \title{visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics
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 \code{ggtree} provides functions for visualizing phylogenetic tree and its associated data in R.}
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 \usage{
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@@ -58,3 +57,4 @@ ggtree(tr)
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 \author{
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 Yu Guangchuang
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 }
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+
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@@ -49,3 +49,4 @@ append a heatmap of a matrix to right side of phylogenetic tree
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -18,3 +18,4 @@
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 \description{
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 groupClade method for ggtree object
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 }
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+
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@@ -20,3 +20,4 @@
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 \description{
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 groupOTU method for ggtree object
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 }
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+
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@@ -3,13 +3,12 @@
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 \docType{methods}
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 \name{gzoom}
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 \alias{gzoom}
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-\alias{gzoom}
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-\alias{gzoom,ggtree-method}
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 \alias{gzoom,beast-method}
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 \alias{gzoom,codeml-method}
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-\alias{gzoom,treedata-method}
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+\alias{gzoom,ggtree-method}
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 \alias{gzoom,paml_rst-method}
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 \alias{gzoom,phylo-method}
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+\alias{gzoom,treedata-method}
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 \title{gzoom method}
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 \usage{
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 gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...)
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@@ -51,3 +50,4 @@ figure
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 \description{
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 zoom selected subtree
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 }
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+
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@@ -29,3 +29,4 @@ gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))
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 \author{
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 ygc
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 }
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+
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@@ -20,3 +20,4 @@ identify node by interactive click
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -35,3 +35,4 @@ add insets in a tree
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -31,3 +31,4 @@ nodes = remove tip nodes.
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32 32
 ```
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 }
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+
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@@ -20,3 +20,4 @@ tree as data.frame with equal angle layout.
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 \references{
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 "Inferring Phylogenies" by Joseph Felsenstein.
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 }
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+
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@@ -28,3 +28,4 @@ multiple sequence alignment with phylogenetic tree
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -29,3 +29,4 @@ plot multiple ggplot objects in one page
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -26,3 +26,4 @@ generate a list of bar charts for results of ancestral state reconstruction
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -20,3 +20,4 @@ convert tip or node label(s) to internal node number
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -24,3 +24,4 @@ generate a list of pie charts for results of ancestral stat reconstruction
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -20,3 +20,4 @@ open tree with specific angle
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 \author{
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 Guangchuang Yu
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 }
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+
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@@ -35,3 +35,4 @@ add phylopic layer
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 \author{
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 Guangchuang Yu
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 }
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+
... ...
@@ -17,3 +17,4 @@ pipe
17 17
 \seealso{
18 18
 \link[magrittr]{pipe}
19 19
 }
20
+
... ...
@@ -20,3 +20,4 @@ print information of a list of beast trees
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
+
... ...
@@ -26,3 +26,4 @@ tree object
26 26
 \description{
27 27
 reroot a tree
28 28
 }
29
+
... ...
@@ -20,3 +20,4 @@ rescale branch length of tree object
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
+
... ...
@@ -18,3 +18,4 @@ reverse timescle x-axis
18 18
 \author{
19 19
 guangchuang yu
20 20
 }
21
+
... ...
@@ -20,3 +20,4 @@ remove singleton
20 20
 \author{
21 21
 Guangchuang Yu \url{http://ygc.name}
22 22
 }
23
+
... ...
@@ -20,3 +20,4 @@ rotate 180 degree of a selected branch
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
+
... ...
@@ -21,3 +21,4 @@ updated tree data.frame with points rotated by angle
21 21
 \description{
22 22
 Rotate the points in a tree data.frame around a pivot node by the angle specified.
23 23
 }
24
+
... ...
@@ -20,3 +20,4 @@ rotate circular tree
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
+
... ...
@@ -26,3 +26,4 @@ scale clade
26 26
 \author{
27 27
 Guangchuang Yu
28 28
 }
29
+
... ...
@@ -4,9 +4,9 @@
4 4
 \name{scale_color}
5 5
 \alias{scale_color}
6 6
 \alias{scale_color,beast-method}
7
-\alias{scale_color,treedata-method}
8 7
 \alias{scale_color,paml_rst-method}
9 8
 \alias{scale_color,phylo-method}
9
+\alias{scale_color,treedata-method}
10 10
 \title{scale_color method}
11 11
 \usage{
12 12
 scale_color(object, by, ...)
... ...
@@ -33,3 +33,4 @@ color vector
33 33
 \description{
34 34
 scale color by a numerical tree attribute
35 35
 }
36
+
... ...
@@ -22,3 +22,4 @@ scale x for tree with heatmap
22 22
 \author{
23 23
 Guangchuang Yu
24 24
 }
25
+
... ...
@@ -41,3 +41,4 @@ layer
41 41
 \description{
42 42
 stat_balance
43 43
 }
44
+
... ...
@@ -39,3 +39,4 @@ layer
39 39
 \description{
40 40
 stat_hilight
41 41
 }
42
+
... ...
@@ -28,3 +28,4 @@ add subview to mainview for ggplot2 objects
28 28
 \author{
29 29
 Guangchuang Yu
30 30
 }
31
+
... ...
@@ -21,3 +21,4 @@ theme for inset function
21 21
 \author{
22 22
 Guangchuang Yu
23 23
 }
24
+
... ...
@@ -18,3 +18,4 @@ transparent background theme
18 18
 \author{
19 19
 Guangchuang Yu
20 20
 }
21
+
... ...
@@ -27,3 +27,4 @@ ggtree(tr) + theme_tree()
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
+
... ...
@@ -27,3 +27,4 @@ ggtree(tr) + theme_tree2()
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
+
... ...
@@ -27,3 +27,4 @@ p \%<\% rtree(30)
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
+
... ...
@@ -22,3 +22,4 @@ view a clade of tree
22 22
 \author{
23 23
 Guangchuang Yu
24 24
 }
25
+
... ...
@@ -20,3 +20,4 @@ expand x axis limits for specific panel
20 20
 \author{
21 21
 guangchuang yu
22 22
 }
23
+
... ...
@@ -18,3 +18,4 @@ set x axis limits for Tree panel
18 18
 \author{
19 19
 guangchuang yu
20 20
 }
21
+