1. ggtree
  2. Commit ae79357644196e14ac50d35ca34c2c7282a2aae2
Browse code

add ctb

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122979 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 24/10/2016 09:29:52
Showing 6 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: 1.7.0
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-Author: Guangchuang Yu and Tommy Tsan-Yuk Lam
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+Version: 1.7.1
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+Authors@R: c(
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+	   person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre")),
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+	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = "aut"),
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+	   person("Justin", "Silverman", email = "jsilve24@gmail.com", rol = "ctb", comment = "geom_balance"),
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+	   person("Casey", "Dunn", email = "casey_dunn@brown.edu", rol = "ctb", comment = "propose using txtConnection so that parser functions can use tree strings as input")
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+	   )
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+Author: Guangchuang Yu <guangchuangyu@gmail.com> and Tommy Tsan-Yuk Lam with contributions from
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+   	Justin Silverman and Casey Dunn.
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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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 	     'ggtree' is designed for visualization and annotation of phylogenetic trees with their covariates and other associated data.
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 Depends:
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-    R (>= 3.3.0),
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-    ggplot2 (>= 2.0.0)
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+    R (>= 3.3.1),
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+    ggplot2 (>= 2.1.0)
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 Imports:
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     ape,
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     grDevices,
NEWS
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+CHANGES IN VERSION 1.7.1
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+------------------------
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+ o make tree stats available in facet_plot <2016-10-24, Mon>
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+
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 CHANGES IN VERSION 1.6.0
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 ------------------------
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  o BioC 3.4 released <2016-10-18, Tue>
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-
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+
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 CHANGES IN VERSION 1.5.17
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 ------------------------
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  o read.nhx support newick file <2016-10-17, Mon>
R/operator.R
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-##' update tree
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+##' update tree
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 ##'
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 ##'
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 ##' @rdname update-TREE
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 ##' @examples
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 ##' nwk <- system.file("extdata", "sample.nwk", package="ggtree")
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 ##' tree <- read.tree(nwk)
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-##' p <- ggtree(tree)
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-##' dd <- data.frame(taxa=LETTERS[1:13],
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+##' p <- ggtree(tree)
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+##' dd <- data.frame(taxa=LETTERS[1:13],
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 ##'    		 place=c(rep("GZ", 5), rep("HK", 3), rep("CZ", 4), NA),
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 ##'              value=round(abs(rnorm(13, mean=70, sd=10)), digits=1))
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 ##' row.names(dd) <- NULL
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@@ -55,8 +55,8 @@
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     right     <- get("right", envir = pg$plot_env)
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     branch.length <- get("branch.length", envir = pg$plot_env)
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     ndigits <- get("ndigits", envir = pg$plot_env)
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-
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-
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+
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+
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     pg$data <- fortify(tree,
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                        layout        = layout,
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                        yscale        = yscale,
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 ##'
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 ##' @rdname add_TREEINFO
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 ##' @title \%+>\%
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-##' @param p tree view
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+##' @param p tree view
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 ##' @param data data.frame
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 ##' @return updated data.frame
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 ##' @export
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 ##' @author Guangchuang Yu
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 `%+>%` <- function(p, data) {
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     df <- p$data
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-    res <- merge(df[, c('label', 'y')], data, by.x='label', by.y=1) ## , all.x=TRUE)
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+    ## res <- merge(df[, c('label', 'y')], data, by.x='label', by.y=1) ## , all.x=TRUE)
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+    res <- merge(df, data, by.x='label', by.y=1) ## , all.x=TRUE)
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     lv <- levels(df$panel)
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     res$panel <- factor(lv[length(lv)], levels=lv)
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     return(res)
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-1.6.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.0-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-15413/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-1.6.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.1-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-15614/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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-[![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--10--19-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--10--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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 [![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-248-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-246-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-15413/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-15614/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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          +-------------------------+------------------------+-------------------------+----------------+
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          |                                                                                         *   |
man/add-TREEDATA.Rd
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 \examples{
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 nwk <- system.file("extdata", "sample.nwk", package="ggtree")
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 tree <- read.tree(nwk)
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-p <- ggtree(tree)
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-dd <- data.frame(taxa=LETTERS[1:13],
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+p <- ggtree(tree)
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+dd <- data.frame(taxa=LETTERS[1:13],
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    		 place=c(rep("GZ", 5), rep("HK", 3), rep("CZ", 4), NA),
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              value=round(abs(rnorm(13, mean=70, sd=10)), digits=1))
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 row.names(dd) <- NULL
vignettes/advanceTreeAnnotation.Rmd
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 # Plot tree with associated data
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-For associating phylogenetic tree with different type of plot produced by user's data, `ggtree` provides `facet_plot` function which accepts an input `data.frame` and a 'geom' function to draw the input data. The data will be displayed in an additional panel of the plot.
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+For associating phylogenetic tree with different type of plot produced by user's data, `ggtree` provides `facet_plot` function which accepts an input `data.frame` and a `geom` function to draw the input data. The data will be displayed in an additional panel of the plot.
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 ```{r warning=F, fig.width=10, fig.height=6}
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 tr <- rtree(30)