1. ggtree
  2. Commit 4fca06a695e1df4f2f3398764083a0265939a6c1
Browse code

update docs

Guangchuang Yu authored on 09/08/2019 03:42:00
Showing 3 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
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-    their covariates and other associated data
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+Title: an R package for visualization of tree and annotation data
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 Version: 1.17.4
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 Authors@R: c(
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 	   person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),
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@@ -14,7 +13,7 @@ Authors@R: c(
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 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
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 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented
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     the grammar of graphics. 'ggtree' is designed for visualization and annotation
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-    of phylogenetic trees with their covariates and other associated data.
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+    of phylogenetic trees and other tree-like structure with their associated data.
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 Depends:
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     R (>= 3.4.0)
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 Imports:
README.Rmd
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@@ -8,7 +8,7 @@ html_preview: false
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 <!-- README.md is generated from README.Rmd. Please edit that file -->
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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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+#  ggtree: an R package for visualization of tree and annotation data
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 ```{r echo=FALSE, results="hide", message=FALSE}
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 #library("txtplot")
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@@ -25,16 +25,18 @@ Biocpkg <- function (pkg) {
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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)
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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)
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 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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-`r badge_bioc_release("ggtree", "green")`
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-`r badge_devel("guangchuangyu/ggtree", "green")`
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+[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+`r badge_bioc_release("ggtree", "green")`
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+`r badge_devel("guangchuangyu/ggtree", "green")`
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 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
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 [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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-`r badge_bioc_download_rank("ggtree")`
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+
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+
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 `r badge_bioc_download("ggtree", "total", "blue")`
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 `r badge_bioc_download("ggtree", "month", "blue")`
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-[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+`r badge_bioc_download_rank("ggtree")`
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 ```{r comment="", echo=FALSE, results='asis'}
README.md
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 <!-- README.md is generated from README.Rmd. Please edit that file -->
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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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+# ggtree: an R package for visualization of tree and annotation data
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-<a href="https://github.com/YuLab-SMU/ggtree"><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></a>
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+<a href="https://yulab-smu.github.io/treedata-book/"><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></a>
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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)
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 [![Project Status: Active - The project has reached a stable, usable
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 state and is being actively
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 developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
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 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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+[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+
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 [![](https://img.shields.io/badge/release%20version-1.16.3-green.svg)](https://www.bioconductor.org/packages/ggtree)
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 [![](https://img.shields.io/badge/devel%20version-1.17.4-green.svg)](https://github.com/guangchuangyu/ggtree)
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-
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 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
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 [![Last-changedate](https://img.shields.io/badge/last%20change-2019--08--09-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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-[![download](http://www.bioconductor.org/shields/downloads/release/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+
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 [![](https://img.shields.io/badge/download-54064/total-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 [![](https://img.shields.io/badge/download-2000/month-blue.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+[![download](http://www.bioconductor.org/shields/downloads/release/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 ‘ggtree’ extends the ‘ggplot2’ plotting system which implemented the
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 grammar of graphics. ‘ggtree’ is designed for visualization and