1. ggtree
  2. Commit a91c9f449fb73bb92990b4eab8e2841effea8d1e
Browse code

update citation

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@126053 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 20/01/2017 05:20:38
Showing 11 changed files
.svnignore
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@@ -6,3 +6,4 @@ appveyor.yml
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 .travis.yml
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 docs
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 mkdocs
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+.gitmodules
DESCRIPTION
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@@ -1,7 +1,7 @@
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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: 1.7.5
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+Version: 1.7.7
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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")),
NEWS
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@@ -1,5 +1,16 @@
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+CHANGES IN VERSION 1.7.7
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+------------------------
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+ o update citation info <2017-01-20, Fri>
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+
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+CHANGES IN VERSION 1.7.6
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+------------------------
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+ o inset support reverse scale <2017-01-05, Thu>
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+   + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/_JPfm71Z8nM/6gL93oxHFQAJ
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+
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 CHANGES IN VERSION 1.7.5
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 ------------------------
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+ o disable labeling collapsed node as tip <2017-01-03, Tue>
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+   + https://groups.google.com/forum/#!topic/bioc-ggtree/nReqJatMvJQ
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  o fortify.phylo4d via converting phylo4d to treedata object <2016-12-28, Wed>
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  o improve viewClade function, use coord_cartesian instead of xlim <2016-12-28, Wed>
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  o remove codes that move to treeio and now ggtree depends treeio <2016-12-20, Tue>
R/clade-functions.R
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@@ -33,12 +33,13 @@ get_taxa_name <- function(tree_view=NULL, node) {
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 ##' @author Guangchuang Yu
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 viewClade <- function(tree_view=NULL, node, xmax_adjust=0) {
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     tree_view %<>% get_tree_view
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+    xd <- tree_view$data$branch.length[node]/2
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     cpos <- get_clade_position(tree_view, node=node)
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     xmax <- ggplot_build(tree_view)$layout$panel_ranges[[1]]$x.range[2]
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     ## tree_view+xlim(cpos$xmin, xmax + xmax_adjust) + ylim(cpos$ymin, cpos$ymax)
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-    tree_view + coord_cartesian(xlim=c(cpos$xmin, xmax), ylim=c(cpos$ymin, cpos$ymax))
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+    tree_view + coord_cartesian(xlim=c(cpos$xmin-xd, xmax), ylim=c(cpos$ymin, cpos$ymax), expand=FALSE)
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 }
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@@ -65,7 +66,7 @@ collapse <- function(tree_view=NULL, node) {
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     sp <- get.offspring.df(df, node)
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     sp.df <- df[sp,]
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-    df[node, "isTip"] <- TRUE
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+    ## df[node, "isTip"] <- TRUE
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     sp_y <- range(sp.df$y, na.rm=TRUE)
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     ii <- which(df$y > max(sp_y))
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     if (length(ii)) {
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@@ -109,7 +110,7 @@ expand <- function(tree_view=NULL, node) {
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         return(tree_view)
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     }
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     df <- tree_view$data
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-    df[node, "isTip"] <- FALSE
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+    ## df[node, "isTip"] <- FALSE
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     sp_y <- range(sp.df$y)
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     ii <- which(df$y > df$y[node])
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     df[ii, "y"] <- df[ii, "y"] + diff(sp_y)
R/inset.R
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@@ -9,10 +9,14 @@
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 ##' @param hjust horizontal adjustment
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 ##' @param vjust vertical adjustment
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 ##' @param x x position, one of 'node' and 'branch'
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+##' @param reverse_x whether x axis was reversed by scale_x_reverse
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+##' @param reverse_y whether y axis was reversed by scale_y_reverse
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 ##' @return tree view with insets
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 ##' @export
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 ##' @author Guangchuang Yu
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-inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0, x="node") {
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+inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0,
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+                  x="node", reverse_x=FALSE, reverse_y=FALSE) {
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+
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     df <- tree_view$data[as.numeric(names(insets)),]
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     x <- match.arg(x, c("node", "branch", "edge"))
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@@ -25,6 +29,10 @@ inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0, x=
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     xx <- xx - hjust
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     yy <- yy - vjust
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+    if (reverse_x)
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+        xx <- -xx
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+    if (reverse_y)
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+        yy <- -yy
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     for (i in seq_along(insets)) {
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         tree_view %<>% subview(insets[[i]],
R/zzz.R
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@@ -7,7 +7,7 @@
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     citation <- paste0("If you use ", pkgname, " in published research, please cite:\n",
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                   "Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ",
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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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-                  "Methods in Ecology and Evolution 2016, doi:10.1111/2041-210X.12628")
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+                  "Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628")
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     packageStartupMessage(paste0(msg, citation))
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 }
README.Rmd
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@@ -45,7 +45,8 @@ The `ggtree` package extending the `ggplot2` package. It based on grammar of gra
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 Please cite the following article when using `ggtree`:
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-__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. 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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+__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36.
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+
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 `r badge_doi("10.1111/2041-210X.12628", "green")`
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 `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
README.md
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@@ -2,9 +2,9 @@
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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-1.6.6-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.5-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-19096/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />
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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.7-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.7-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-20046/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1177/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--12--30-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--01--20-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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@@ -16,9 +16,9 @@ The `ggtree` package extending the `ggplot2` package. It based on grammar of gra
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 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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+**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***. 2017, 8(1):28-36.
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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-284-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-299-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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 ------------------------------------------------------------------------
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@@ -51,30 +51,30 @@ 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-19096/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1852/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-20046/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1177/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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+     500 +                             *                                                               +
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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                  2017
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+       0 +   *   *  *                                                                                  +
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+         ++---------------------+---------------------+---------------------+---------------------+----+
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+        2015                 2015.5                 2016                 2016.5                 2017
inst/CITATION
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@@ -10,17 +10,17 @@ citEntry(
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         as.person("Yi Guan"),
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         as.person("Tommy Tsan-Yuk Lam")
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         ),
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-    year    = "accepted",
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+    year    = "2017",
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     journal = "Methods in Ecology and Evolution",
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-    volume  = "",
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-    issue   = "",
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+    volume  = "8",
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+    issue   = "1",
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     number  = "",
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-    pages   = "",
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+    pages   = "28-36",
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     doi     = "10.1111/2041-210X.12628",
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     PMID    = "",
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-    url     = "",
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+    url     = "http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract",
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     textVersion = paste("Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.",
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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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-        "Methods in Ecology and Evolution 2016 accepted, doi:10.1111/2041-210X.12628")
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+        "Methods in Ecology and Evolution 2017, 8(1):28-36")
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 )
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man/inset.Rd
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@@ -5,7 +5,7 @@
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 \title{inset}
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 \usage{
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 inset(tree_view, insets, width = 0.1, height = 0.1, hjust = 0,
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-  vjust = 0, x = "node")
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+  vjust = 0, x = "node", reverse_x = FALSE, reverse_y = FALSE)
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 }
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 \arguments{
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 \item{tree_view}{tree view}
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 \item{vjust}{vertical adjustment}
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 \item{x}{x position, one of 'node' and 'branch'}
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+
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+\item{reverse_x}{whether x axis was reversed by scale_x_reverse}
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+\item{reverse_y}{whether y axis was reversed by scale_y_reverse}
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 }
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 \value{
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 tree view with insets
vignettes/ggtree.Rmd
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@@ -40,9 +40,10 @@ library("ggtree")
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 # Citation
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+
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 If you use `ggtree` in published research, please cite:
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-__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. _accepted_. doi:[10.1111/2041-210X.12628](http://dx.doi.org/10.1111/2041-210X.12628)
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+__G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. __*Methods in Ecology and Evolution*__. 2017, 8(1):28-36. doi:[10.1111/2041-210X.12628](http://dx.doi.org/10.1111/2041-210X.12628)
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 # Introduction