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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@131307 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 18/07/2017 07:59:43
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+# Contribute
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+
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+## Introduction
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+
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+First, thank you for considering contributing to ggtree! It's people like you that make the open source community such a great community! 😊
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+
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+We welcome any type of contribution, not only code. You can help with 
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+- **QA**: file bug reports, the more details you can give the better (e.g. screenshots with the console open)
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+- **Marketing**: writing blog posts, howto's, printing stickers, ...
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+- **Community**: presenting the project at meetups, organizing a dedicated meetup for the local community, ...
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+- **Code**: take a look at the [open issues](issues). Even if you can't write code, commenting on them, showing that you care about a given issue matters. It helps us triage them.
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+- **Money**: we welcome financial contributions in full transparency on our [open collective](https://opencollective.com/ggtree).
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+
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+## Your First Contribution
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+
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+Working on your first Pull Request? You can learn how from this *free* series, [How to Contribute to an Open Source Project on GitHub](https://egghead.io/series/how-to-contribute-to-an-open-source-project-on-github).
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+
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+## Submitting code
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+
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+Any code change should be submitted as a pull request. The description should explain what the code does and give steps to execute it. The pull request should also contain tests.
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+
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+## Code review process
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+
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+The bigger the pull request, the longer it will take to review and merge. Try to break down large pull requests in smaller chunks that are easier to review and merge.
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+It is also always helpful to have some context for your pull request. What was the purpose? Why does it matter to you?
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+
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+## Financial contributions
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+
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+We also welcome financial contributions in full transparency on our [open collective](https://opencollective.com/ggtree).
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+Anyone can file an expense. If the expense makes sense for the development of the community, it will be "merged" in the ledger of our open collective by the core contributors and the person who filed the expense will be reimbursed.
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+
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+## Questions
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+
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+If you have any questions, create an [issue](issue) (protip: do a quick search first to see if someone else didn't ask the same question before!).
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+You can also reach us at hello@ggtree.opencollective.com.
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+
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+## Credits
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+
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+### Contributors
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+
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+Thank you to all the people who have already contributed to ggtree!
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+<a href="graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a>
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+
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+
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+### Backers
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+
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+Thank you to all our backers! [[Become a backer](https://opencollective.com/ggtree#backer)]
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+
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+<a href="https://opencollective.com/ggtree#backers" target="_blank"><img src="https://opencollective.com/ggtree/backers.svg?width=890"></a>
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+
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+
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+### Sponsors
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+
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+Thank you to all our sponsors! (please ask your company to also support this open source project by [becoming a sponsor](https://opencollective.com/ggtree#sponsor))
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+
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+<a href="https://opencollective.com/ggtree/sponsor/0/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/0/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/1/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/1/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/2/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/2/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/3/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/3/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/4/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/4/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/5/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/5/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/6/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/6/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/7/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/7/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/8/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/8/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/9/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/9/avatar.svg"></a>
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+
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+<!-- This `CONTRIBUTING.md` is based on @nayafia's template https://github.com/nayafia/contributing-template -->
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\ No newline at end of file
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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: 5.0.1
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+RoxygenNote: 6.0.1
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@@ -70,3 +70,8 @@ svncommit:
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 	git push -u origin devel;\
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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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@@ -14,6 +14,8 @@ 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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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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@@ -37,7 +39,8 @@ library("ypages")
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 [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/)
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 [![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)
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 [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree)
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-
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+[![Backers on Open Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers)
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+[![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)
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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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@@ -74,9 +77,16 @@ __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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+## 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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+    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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+
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+<img src="docs/citation.png" width="890"/>
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+
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+
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 ### Download stats
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 `r badge_download_bioc("ggtree")`
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@@ -84,13 +94,45 @@ txtplot(d$year, d$cites)
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 `r badge_bioc_download("ggtree", "month", "blue")`
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-```{r echo=F, comment=NA}
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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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+## 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/dlstats.png", width=8, height=4)
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 ```
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+<img src="docs/dlstats.png" width="890"/>
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+
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+## Contributors
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+
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+This project exists thanks to all the people who contribute. [[Contribute]](CONTRIBUTING.md).
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+<a href="https://github.com/GuangchuangYu/ggtree/graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a>
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+
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+
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+## Backers
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+
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+Thank you to all our backers! 🙏 [[Become a backer](https://opencollective.com/ggtree#backer)]
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+
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+<a href="https://opencollective.com/ggtree#backers" target="_blank"><img src="https://opencollective.com/ggtree/backers.svg?width=890"></a>
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+
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+
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+## Sponsors
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+
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+Support this project by becoming a sponsor. Your logo will show up here with a link to your website. [[Become a sponsor](https://opencollective.com/ggtree#sponsor)]
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+<a href="https://opencollective.com/ggtree/sponsor/0/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/0/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/1/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/1/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/2/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/2/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/3/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/3/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/4/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/4/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/5/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/5/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/6/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/6/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/7/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/7/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/8/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/8/avatar.svg"></a>
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+<a href="https://opencollective.com/ggtree/sponsor/9/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/9/avatar.svg"></a>
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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-1.9.1-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) [![](https://img.shields.io/badge/download-16674/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1117/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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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--06--29-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--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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-[![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)
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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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 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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 **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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+[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![](https://img.shields.io/badge/Altmetric-349-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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 ------------------------------------------------------------------------
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 ### Citation
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-[![citation](https://img.shields.io/badge/cited%20by-22-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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+[![citation](https://img.shields.io/badge/cited%20by-26-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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+<img src="docs/citation.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) [![](https://img.shields.io/badge/download-16674/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1117/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-        2015              2015.5             2016             2016.5             2017            2017.5
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+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](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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+<img src="docs/dlstats.png" width="890"/>
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+
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+Contributors
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+------------
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+
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+This project exists thanks to all the people who contribute. [\[Contribute\]](CONTRIBUTING.md). <a href="https://github.com/GuangchuangYu/ggtree/graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a>
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+
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+Backers
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+-------
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+
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+Thank you to all our backers! 🙏 \[[Become a backer](https://opencollective.com/ggtree#backer)\]
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+
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+<a href="https://opencollective.com/ggtree#backers" target="_blank"><img src="https://opencollective.com/ggtree/backers.svg?width=890"></a>
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+
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+Sponsors
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+--------
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+
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+Support this project by becoming a sponsor. Your logo will show up here with a link to your website. \[[Become a sponsor](https://opencollective.com/ggtree#sponsor)\]
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+
63
+<a href="https://opencollective.com/ggtree/sponsor/0/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/0/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/1/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/1/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/2/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/2/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/3/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/3/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/4/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/4/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/5/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/5/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/6/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/6/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/7/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/7/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/8/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/8/avatar.svg"></a> <a href="https://opencollective.com/ggtree/sponsor/9/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/9/avatar.svg"></a>
... ...
@@ -18,4 +18,3 @@ convert Date to decimal format, eg "2014-05-05" to "2014.34"
18 18
 \author{
19 19
 Guangchuang Yu
20 20
 }
21
-
... ...
@@ -17,4 +17,3 @@ list of all child node id's from starting node.
17 17
 \description{
18 18
 Get all children of node from df tree using breath-first.
19 19
 }
20
-
... ...
@@ -18,4 +18,3 @@ named list of subtrees with the root id of subtree and list of node id's making
18 18
 Get all subtrees of specified node. This includes all ancestors and relatives of node and
19 19
 return named list of subtrees.
20 20
 }
21
-
... ...
@@ -20,4 +20,3 @@ Find Most Recent Common Ancestor among a vector of tips
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -31,4 +31,3 @@ print(tree)
31 31
 \author{
32 32
 ygc
33 33
 }
34
-
... ...
@@ -30,4 +30,3 @@ p \%<+\% dd + geom_text(aes(color=place, label=label), hjust=-0.5)
30 30
 \author{
31 31
 Yu Guangchuang
32 32
 }
33
-
... ...
@@ -20,4 +20,3 @@ update data with tree info (y coordination and panel)
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -29,4 +29,3 @@ add colorbar legend
29 29
 \author{
30 30
 Guangchuang Yu
31 31
 }
32
-
... ...
@@ -31,4 +31,3 @@ annotation taxa with images
31 31
 \author{
32 32
 Guangchuang Yu
33 33
 }
34
-
... ...
@@ -20,4 +20,3 @@ merge phylo and output of boot.phylo to 'apeBootstrap' object
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -18,4 +18,3 @@ list with tree data.frame with updated layout using daylight algorithm and max_c
18 18
 Apply the daylight alorithm to adjust the spacing between the subtrees and tips of the
19 19
 specified node.
20 20
 }
21
-
... ...
@@ -30,4 +30,3 @@ is.binary.tree(tr2)
30 30
 \author{
31 31
 Guangchuang Yu \url{http://ygc.name}
32 32
 }
33
-
... ...
@@ -27,4 +27,3 @@ convert phylo to data.frame
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
-
... ...
@@ -22,4 +22,3 @@ collapse binary tree to polytomy by applying 'fun' to 'feature'
22 22
 \author{
23 23
 Guangchuang
24 24
 }
25
-
... ...
@@ -17,10 +17,9 @@ tree view
17 17
 \description{
18 18
 collapse a clade
19 19
 }
20
-\author{
21
-Guangchuang Yu
22
-}
23 20
 \seealso{
24 21
 expand
25 22
 }
26
-
23
+\author{
24
+Guangchuang Yu
25
+}
... ...
@@ -18,4 +18,3 @@ convert decimal format to Date, eg "2014.34" to "2014-05-05"
18 18
 \author{
19 19
 Guangchuang Yu
20 20
 }
21
-
... ...
@@ -21,4 +21,3 @@ capture name of variable
21 21
 x <- 1
22 22
 eval(.(x)[[1]])
23 23
 }
24
-
... ...
@@ -24,4 +24,3 @@ download phylopic
24 24
 \author{
25 25
 Guangchuang Yu
26 26
 }
27
-
... ...
@@ -17,10 +17,9 @@ tree view
17 17
 \description{
18 18
 expand collased clade
19 19
 }
20
-\author{
21
-Guangchuang Yu
22
-}
23 20
 \seealso{
24 21
 collapse
25 22
 }
26
-
23
+\author{
24
+Guangchuang Yu
25
+}
... ...
@@ -28,4 +28,3 @@ plot tree associated data in an additional panel
28 28
 \author{
29 29
 Guangchuang Yu
30 30
 }
31
-
... ...
@@ -22,4 +22,3 @@ flip position of two selected branches
22 22
 \author{
23 23
 Guangchuang Yu
24 24
 }
25
-
... ...
@@ -33,4 +33,3 @@ fortify a phylo to data.frame
33 33
 \author{
34 34
 Yu Guangchuang
35 35
 }
36
-
... ...
@@ -24,4 +24,3 @@ add horizontal align lines
24 24
 \author{
25 25
 Yu Guangchuang
26 26
 }
27
-
... ...
@@ -30,11 +30,10 @@ highlights the two direct descendant clades of an internal node
30 30
 Particularly useful when studying neighboring clades. Note that balances that
31 31
 correspond to multichotomies will not be displayed.
32 32
 }
33
-\author{
34
-Justin Silverman
35
-}
36 33
 \references{
37 34
 J. Silverman, et al. \emph{A phylogenetic transform enhances
38 35
   analysis of compositional microbiota data}. (in preparation)
39 36
 }
40
-
37
+\author{
38
+Justin Silverman
39
+}
... ...
@@ -48,4 +48,3 @@ annotate a clade with bar and text label
48 48
 \author{
49 49
 Guangchuang Yu
50 50
 }
51
-
... ...
@@ -27,4 +27,3 @@ layer of hilight clade with rectangle
27 27
 \author{
28 28
 Guangchuang Yu
29 29
 }
30
-
... ...
@@ -45,10 +45,9 @@ label layer
45 45
 \description{
46 46
 geom_label2 support aes(subset) via setup_data
47 47
 }
48
-\author{
49
-Guangchuang Yu
50
-}
51 48
 \seealso{
52 49
 \link[ggplot2]{geom_label}
53 50
 }
54
-
51
+\author{
52
+Guangchuang Yu
53
+}
... ...
@@ -31,4 +31,3 @@ add node point
31 31
 \author{
32 32
 Guangchuang Yu
33 33
 }
34
-
... ...
@@ -28,10 +28,9 @@ point layer
28 28
 \description{
29 29
 geom_point2 support aes(subset) via setup_data
30 30
 }
31
-\author{
32
-Guangchuang Yu
33
-}
34 31
 \seealso{
35 32
 \link[ggplot2]{geom_point}
36 33
 }
37
-
34
+\author{
35
+Guangchuang Yu
36
+}
... ...
@@ -20,4 +20,3 @@ bar of range (HPD, range etc) to present uncertainty of evolutionary inference
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -31,4 +31,3 @@ add root point
31 31
 \author{
32 32
 Guangchuang Yu
33 33
 }
34
-
... ...
@@ -33,10 +33,9 @@ add segment layer
33 33
 \description{
34 34
 geom_segment2 support aes(subset) via setup_data
35 35
 }
36
-\author{
37
-Guangchuang Yu
38
-}
39 36
 \seealso{
40 37
 \link[ggplot2]{geom_segment}
41 38
 }
42
-
39
+\author{
40
+Guangchuang Yu
41
+}
... ...
@@ -51,4 +51,3 @@ annotate associated taxa (from taxa1 to taxa2, can be Monophyletic, Polyphyletic
51 51
 \author{
52 52
 Guangchuang Yu
53 53
 }
54
-
... ...
@@ -26,4 +26,3 @@ link between taxa
26 26
 \author{
27 27
 Guangchuang Yu
28 28
 }
29
-
... ...
@@ -40,10 +40,9 @@ text layer
40 40
 \description{
41 41
 geom_text2 support aes(subset) via setup_data
42 42
 }
43
-\author{
44
-Guangchuang Yu
45
-}
46 43
 \seealso{
47 44
 \link[ggplot2]{geom_text}
48 45
 }
49
-
46
+\author{
47
+Guangchuang Yu
48
+}
... ...
@@ -38,4 +38,3 @@ ggtree(tr) + geom_tiplab()
38 38
 \author{
39 39
 Yu Guangchuang
40 40
 }
41
-
... ...
@@ -19,10 +19,9 @@ tip label layer
19 19
 \description{
20 20
 add tip label for circular layout
21 21
 }
22
-\author{
23
-Guangchuang Yu
24
-}
25 22
 \references{
26 23
 \url{https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0}
27 24
 }
28
-
25
+\author{
26
+Guangchuang Yu
27
+}
... ...
@@ -31,4 +31,3 @@ add tip point
31 31
 \author{
32 32
 Guangchuang Yu
33 33
 }
34
-
... ...
@@ -27,4 +27,3 @@ add tree layer
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
-
... ...
@@ -20,4 +20,3 @@ add tree layer
20 20
 \author{
21 21
 Yu Guangchuang
22 22
 }
23
-
... ...
@@ -33,4 +33,3 @@ add tree scale
33 33
 \author{
34 34
 Guangchuang Yu
35 35
 }
36
-
... ...
@@ -20,4 +20,3 @@ extract offspring tips
20 20
 \author{
21 21
 ygc
22 22
 }
23
-
... ...
@@ -22,4 +22,3 @@ path from start node to end node
22 22
 \author{
23 23
 Guangchuang Yu
24 24
 }
25
-
... ...
@@ -24,4 +24,3 @@ download phylopic and convert to grob object
24 24
 \author{
25 25
 Guangchuang Yu
26 26
 }
27
-
... ...
@@ -17,4 +17,3 @@ list of child node ids of parent
17 17
 \description{
18 18
 Get list of child node id numbers of parent node
19 19
 }
20
-
... ...
@@ -19,4 +19,3 @@ angle in range [-1, 1], i.e. degrees/180, radians/pi
19 19
 \description{
20 20
 Get the angle between the two nodes specified.
21 21
 }
22
-
... ...
@@ -15,4 +15,3 @@ list of node id's in breadth-first order.
15 15
 \description{
16 16
 Get the nodes of tree from root in breadth-first order.
17 17
 }
18
-
... ...
@@ -17,4 +17,3 @@ integer node id of parent
17 17
 \description{
18 18
 Get parent node id of child node.
19 19
 }
20
-
... ...
@@ -17,4 +17,3 @@ list of all child node id's from starting node.
17 17
 \description{
18 18
 Get all children of node from tree, including start_node.
19 19
 }
20
-
... ...
@@ -18,4 +18,3 @@ named list of subtrees with the root id of subtree and list of node id's making
18 18
 Get all subtrees of node, as well as remaining branches of parent (ie, rest of tree structure as subtree)
19 19
 return named list of subtrees with list name as starting node id.
20 20
 }
21
-
... ...
@@ -20,4 +20,3 @@ named list with right and left angles in range [0,2] i.e 1 = 180 degrees, 1.5 =
20 20
 Find the right (clockwise rotation, angle from +ve x-axis to furthest subtree nodes) and
21 21
 left (anti-clockwise angle from +ve x-axis to subtree)
22 22
 }
23
-
... ...
@@ -22,4 +22,3 @@ get position of balance (xmin, xmax, ymin, ymax)
22 22
 \author{
23 23
 Justin Silverman
24 24
 }
25
-
... ...
@@ -20,4 +20,3 @@ get position of clade (xmin, xmax, ymin, ymax)
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -21,4 +21,3 @@ for labeling column names of heatmap produced by `gheatmap` function
21 21
 \author{
22 22
 Guangchuang Yu
23 23
 }
24
-
... ...
@@ -20,4 +20,3 @@ get taxa name of a selected node (or tree if node=NULL) sorted by their position
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -11,4 +11,3 @@ StatBalance
11 11
 StatHilight
12 12
 }
13 13
 \keyword{datasets}
14
-
... ...
@@ -3,8 +3,9 @@
3 3
 \docType{package}
4 4
 \name{ggtree}
5 5
 \alias{ggtree}
6
-\alias{ggtree-package}
7 6
 \alias{package-ggtree}
7
+\alias{ggtree-package}
8
+\alias{ggtree}
8 9
 \title{visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics
9 10
 \code{ggtree} provides functions for visualizing phylogenetic tree and its associated data in R.}
10 11
 \usage{
... ...
@@ -57,4 +58,3 @@ ggtree(tr)
57 58
 \author{
58 59
 Yu Guangchuang
59 60
 }
60
-
... ...
@@ -49,4 +49,3 @@ append a heatmap of a matrix to right side of phylogenetic tree
49 49
 \author{
50 50
 Guangchuang Yu
51 51
 }
52
-
... ...
@@ -18,4 +18,3 @@
18 18
 \description{
19 19
 groupClade method for ggtree object
20 20
 }
21
-
... ...
@@ -20,4 +20,3 @@
20 20
 \description{
21 21
 groupOTU method for ggtree object
22 22
 }
23
-
... ...
@@ -3,12 +3,13 @@
3 3
 \docType{methods}
4 4
 \name{gzoom}
5 5
 \alias{gzoom}
6
+\alias{gzoom}
7
+\alias{gzoom,ggtree-method}
6 8
 \alias{gzoom,beast-method}
7 9
 \alias{gzoom,codeml-method}
8
-\alias{gzoom,ggtree-method}
10
+\alias{gzoom,treedata-method}
9 11
 \alias{gzoom,paml_rst-method}
10 12
 \alias{gzoom,phylo-method}
11
-\alias{gzoom,treedata-method}
12 13
 \title{gzoom method}
13 14
 \usage{
14 15
 gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...)
... ...
@@ -50,4 +51,3 @@ figure
50 51
 \description{
51 52
 zoom selected subtree
52 53
 }
53
-
... ...
@@ -29,4 +29,3 @@ gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))
29 29
 \author{
30 30
 ygc
31 31
 }
32
-
... ...
@@ -20,4 +20,3 @@ identify node by interactive click
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -35,4 +35,3 @@ add insets in a tree
35 35
 \author{
36 36
 Guangchuang Yu
37 37
 }
38
-
... ...
@@ -31,4 +31,3 @@ nodes = remove tip nodes.
31 31
 
32 32
 ```
33 33
 }
34
-
... ...
@@ -20,4 +20,3 @@ tree as data.frame with equal angle layout.
20 20
 \references{
21 21
 "Inferring Phylogenies" by Joseph Felsenstein.
22 22
 }
23
-
... ...
@@ -28,4 +28,3 @@ multiple sequence alignment with phylogenetic tree
28 28
 \author{
29 29
 Guangchuang Yu
30 30
 }
31
-
... ...
@@ -29,4 +29,3 @@ plot multiple ggplot objects in one page
29 29
 \author{
30 30
 Guangchuang Yu
31 31
 }
32
-
... ...
@@ -26,4 +26,3 @@ generate a list of bar charts for results of ancestral state reconstruction
26 26
 \author{
27 27
 Guangchuang Yu
28 28
 }
29
-
... ...
@@ -20,4 +20,3 @@ convert tip or node label(s) to internal node number
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -24,4 +24,3 @@ generate a list of pie charts for results of ancestral stat reconstruction
24 24
 \author{
25 25
 Guangchuang Yu
26 26
 }
27
-
... ...
@@ -20,4 +20,3 @@ open tree with specific angle
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -35,4 +35,3 @@ add phylopic layer
35 35
 \author{
36 36
 Guangchuang Yu
37 37
 }
38
-
... ...
@@ -17,4 +17,3 @@ pipe
17 17
 \seealso{
18 18
 \link[magrittr]{pipe}
19 19
 }
20
-
... ...
@@ -20,4 +20,3 @@ print information of a list of beast trees
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -26,4 +26,3 @@ tree object
26 26
 \description{
27 27
 reroot a tree
28 28
 }
29
-
... ...
@@ -20,4 +20,3 @@ rescale branch length of tree object
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -18,4 +18,3 @@ reverse timescle x-axis
18 18
 \author{
19 19
 guangchuang yu
20 20
 }
21
-
... ...
@@ -20,4 +20,3 @@ remove singleton
20 20
 \author{
21 21
 Guangchuang Yu \url{http://ygc.name}
22 22
 }
23
-
... ...
@@ -20,4 +20,3 @@ rotate 180 degree of a selected branch
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -21,4 +21,3 @@ 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
-
... ...
@@ -20,4 +20,3 @@ rotate circular tree
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -26,4 +26,3 @@ 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}
7 8
 \alias{scale_color,paml_rst-method}
8 9
 \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, ...)
... ...
@@ -33,4 +33,3 @@ color vector
33 33
 \description{
34 34
 scale color by a numerical tree attribute
35 35
 }
36
-
... ...
@@ -22,4 +22,3 @@ scale x for tree with heatmap
22 22
 \author{
23 23
 Guangchuang Yu
24 24
 }
25
-
... ...
@@ -41,4 +41,3 @@ layer
41 41
 \description{
42 42
 stat_balance
43 43
 }
44
-
... ...
@@ -39,4 +39,3 @@ layer
39 39
 \description{
40 40
 stat_hilight
41 41
 }
42
-
... ...
@@ -28,4 +28,3 @@ add subview to mainview for ggplot2 objects
28 28
 \author{
29 29
 Guangchuang Yu
30 30
 }
31
-
... ...
@@ -21,4 +21,3 @@ theme for inset function
21 21
 \author{
22 22
 Guangchuang Yu
23 23
 }
24
-
... ...
@@ -18,4 +18,3 @@ transparent background theme
18 18
 \author{
19 19
 Guangchuang Yu
20 20
 }
21
-
... ...
@@ -27,4 +27,3 @@ ggtree(tr) + theme_tree()
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
-
... ...
@@ -27,4 +27,3 @@ ggtree(tr) + theme_tree2()
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
-
... ...
@@ -27,4 +27,3 @@ p \%<\% rtree(30)
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
-
... ...
@@ -22,4 +22,3 @@ view a clade of tree
22 22
 \author{
23 23
 Guangchuang Yu
24 24
 }
25
-
... ...
@@ -20,4 +20,3 @@ expand x axis limits for specific panel
20 20
 \author{
21 21
 guangchuang yu
22 22
 }
23
-
... ...
@@ -18,4 +18,3 @@ set x axis limits for Tree panel
18 18
 \author{
19 19
 guangchuang yu
20 20
 }
21
-