1. ggtree
  2. Commit 7918c8b0b3176d9456297ac0c7215b0eb0da0aeb
Browse code

mv site to http://guangchuangyu.github.io/software/ggtree

guangchuang yu authored on 05/03/2018 04:11:48
Showing 4 changed files
README.Rmd
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@@ -66,13 +66,8 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali
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 ### Citation
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-```{r echo=F, comment=NA}
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-p <- plot_citation_trend('DO5oG40AAAAJ', 'HtEfBTGE9r8C')
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-ggsave(p, file="docs/images/citation.png", width=8, height=4)
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-```
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-
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-<img src="docs/images/citation.png" width="890"/>
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+<img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
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 ### Download stats
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@@ -82,17 +77,7 @@ ggsave(p, file="docs/images/citation.png", width=8, height=4)
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 `r badge_bioc_download("ggtree", "month", "blue")`
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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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-## txtplot(ggtree::Date2decimal(x$end), x$Nb_of_downloads, width=100, height=25)
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-p <- ggplot(x, aes(end, Nb_of_distinct_IPs)) + geom_point() + geom_line() +
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-    theme_minimal() +xlab(NULL) + ylab(NULL) +
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-    labs(title="ggtree", subtitle="Monthly download stats (distinct IPs)", caption="data from Bioconductor")
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-ggsave(p, file="docs/images/dlstats.png", width=8, height=4)
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-```
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-
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-<img src="docs/images/dlstats.png" width="890"/>
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+<img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>
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README.md
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@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.4-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.5-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) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)
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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.5-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.6-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) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays) [![Say Thanks!](https://img.shields.io/badge/Say%20Thanks-!-1EAEDB.svg)](https://saythanks.io/to/GuangchuangYu)
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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) [![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-2018--02--23-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)
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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) [![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-2018--03--05-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)
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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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@@ -25,16 +25,16 @@ 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***. 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) [![Altmetric](https://img.shields.io/badge/Altmetric-326-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-85-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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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) [![Altmetric](https://img.shields.io/badge/Altmetric-328-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-89-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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 ------------------------------------------------------------------------
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 ### Citation
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-<img src="docs/images/citation.png" width="890"/>
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+<img src="https://guangchuangyu.github.io/software/ggtree/featured-articles/index_files/figure-html/citation-1.png" width="890"/>
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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-24849/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1222/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-25396/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1211/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-<img src="docs/images/dlstats.png" width="890"/>
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+<img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>
vignettes/ggtree.Rmd
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@@ -224,8 +224,8 @@ the [Tree Annotation](treeAnnotation.html) vignette.
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 + [Tree Manipulation](treeManipulation.html)
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 + [Tree Annotation](treeAnnotation.html)
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 + [Phylomoji](https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html)
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-+ [Annotating phylogenetic tree with images](https://guangchuangyu.github.io/ggtree/vignettes/ggtree-ggimage.html)
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-+ [Annotate a phylogenetic tree with insets](https://guangchuangyu.github.io/ggtree/vignettes/ggtree-inset.html)
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++ [Annotating phylogenetic tree with images](https://guangchuangyu.github.io/software/ggtree/vignettes/ggtree-ggimage.html)
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++ [Annotate a phylogenetic tree with insets](https://guangchuangyu.github.io/software/ggtree/vignettes/ggtree-inset.html)
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 **ggtree homepage**: <https://guangchuangyu.github.io/ggtree> (contains more
vignettes/treeAnnotation.Rmd
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@@ -330,8 +330,8 @@ facet_plot(p2, panel='bar', data=d2, geom=geom_segment, aes(x=0, xend=value, y=y
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 Please refer to the following vignettes:
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-+ [Annotating phylogenetic tree with images](https://guangchuangyu.github.io/ggtree/vignettes/ggtree-ggimage.html)
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-+ [Annotate a phylogenetic tree with insets](https://guangchuangyu.github.io/ggtree/vignettes/ggtree-inset.html)
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++ [Annotating phylogenetic tree with images](https://guangchuangyu.github.io/software/ggtree/vignettes/ggtree-ggimage.html)
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++ [Annotate a phylogenetic tree with insets](https://guangchuangyu.github.io/software/ggtree/vignettes/ggtree-inset.html)
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