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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@122175 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 11/10/2016 02:01:09
Showing 70 changed files

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 __init__.py
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 __pycache__
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 __init__.pyc
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+Makefile
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+TODO.md
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+appveyor.yml
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+.travis.yml
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+README.Rmd
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+docs
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-## reference: http://docs.travis-ci.com/user/languages/r/
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-
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-language: r
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-r:
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-  - bioc-devel
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-  
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-cache: packages
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-bioc_required: true
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-
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-os:
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-  - linux
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-  - osx
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-
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-apt_packages:
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-  - libfftw3-dev
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-
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-env:
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-  global:
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-    - _R_CHECK_FORCE_SUGGESTS_=False
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-    - R_LIBS="http://cran.rstudio.com"
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-
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-  
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-after_failure:
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-  - ./travis-tool.sh dump_logs
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-
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-r_github_packages:
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-  - jimhester/covr
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-
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-after_success:
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-- Rscript -e 'library(covr); codecov()'
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-
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-## notifications:
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-##   email:
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-##     on_success: change
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-##     on_failure: change
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-PKGNAME := $(shell sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION)
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-PKGVERS := $(shell sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION)
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-PKGSRC  := $(shell basename `pwd`)
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-
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-all: rd readme check clean
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-alldocs: rd readme mkdocs
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-rd:
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-	Rscript -e 'roxygen2::roxygenise(".")'
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-readme:
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-	Rscript -e 'rmarkdown::render("README.Rmd")'
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-build:
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-	cd ..;\
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-	R CMD build $(PKGSRC)
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-build2:
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-	cd ..;\
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-	R CMD build --no-build-vignettes $(PKGSRC)
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-install:
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-	cd ..;\
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-	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
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-check: build
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-	cd ..;\
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-	Rscript -e 'rcmdcheck::rcmdcheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
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-check2: build
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-	cd ..;\
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-	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz
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-bioccheck:
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-	cd ..;\
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-	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'
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-clean:
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-	cd ..;\
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-	$(RM) -r $(PKGNAME).Rcheck/
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-site: mkdocs
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-	cd mkdocs;\
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-	mkdocs build;\
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-	cd mkdocs;\
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-	Rscript -e 'library(ypages); gendoc("private/index.md", "blue", "docs/index.md")';\
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-	Rscript -e 'library(ypages); gendoc("private/documentation.md", "blue", "docs/documentation.md")';\
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-	Rscript -e 'library(ypages); gendoc("private/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
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-	Rscript -e 'library(ypages); gendoc("private/faq.md", "blue", "docs/faq.md")';\
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-	cd docs;\
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-	ln -f -s ../mysoftware/* ./
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-svnignore:
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-	svn propset svn:ignore -F .svnignore .
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-output:
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-  md_document:
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-    variant: markdown_github
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-html_preview: false
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-
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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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-```{r echo=FALSE, results="hide", message=FALSE}
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-library("txtplot")
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-library("ypages")
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-```
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-
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-`r badge_release("ggtree", "green")`
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-`r badge_devel("ggtree", "green")`
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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_download("ggtree", "total", "blue")`
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-`r badge_download("ggtree", "month", "blue")`
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-
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-
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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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-[![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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-[![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network)
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-[![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
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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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-[![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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-[![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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-[![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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-
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-
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-
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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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-
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-[![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ggtree.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)
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-
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-
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-Please cite the following article when using `ggtree`:
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-
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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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-
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-`r badge_doi("10.1111/2041-210X.12628", "green")`
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-`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
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-`r badge_altmetric("10533079", "green")`
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-
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-
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-For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.
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-
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-+ [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)
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-+ [FAQ](https://guangchuangyu.github.io/ggtree/faq/)
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-+ [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)
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-+ [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)
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-
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-### Citation
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-
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-`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
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-
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-
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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$cites, xlim=c(2015, 2017))
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-```
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-
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-### Download stats
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-
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-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/)
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-`r badge_download("ggtree", "total", "blue")`
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-`r badge_download("ggtree", "month", "blue")`
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-
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-
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-```{r echo=F, comment=NA}
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-x <- dlstats::bioc_stats("ggtree")
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-x <- x[-nrow(x), ] # last month data is not complete
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-txtplot(ggtree::Date2decimal(x$end), x$Nb_of_downloads, width=100, height=25)
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-```
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-+ attach user specific data to existing tree object
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-+ attach user specific data by node number
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-+ mask function that accepts tree object, feature name and a function that specific how to mask.
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-  with this function, user can mask some of the features that are not needed to display on a tree.
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-+ defined a function, compare_sequence, that accept a function that defined sequence feature,
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-  and compare the feature from parent to children and add store the info in tree object.
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-  So with ancestral sequences inferred by HYPHY or PAML, we can support any type of sequence feature comparison,
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-  not only substitution supported internally.
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-+ support more features that can be plotted at the right hand side of the tree.
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-  - ~~multiple sequence alignment~~ _Now implemented in 1.1.7_
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-  
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-environment:
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-  matrix:
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-    - R_VERSION: devel
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-      R_ARCH: x64
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-      USE_RTOOLS: true
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-  _R_CHECK_FORCE_SUGGESTS_: false
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-
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-# DO NOT CHANGE the "init" and "install" sections below
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-
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-# Download script file from GitHub
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-init:
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-  ps: |
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-        $ErrorActionPreference = "Stop"
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-        Invoke-WebRequest http://raw.github.com/krlmlr/r-appveyor/master/scripts/appveyor-tool.ps1 -OutFile "..\appveyor-tool.ps1"
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-        Import-Module '..\appveyor-tool.ps1'
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-install:
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-  ps: Bootstrap
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-
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-# Adapt as necessary starting from here
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-
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-build_script:
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-  - travis-tool.sh install_bioc BiocStyle Biostrings  
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-  - travis-tool.sh install_deps
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-test_script:
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-  - travis-tool.sh run_tests
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-on_failure:
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-  - 7z a failure.zip *.Rcheck\*
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-  - appveyor PushArtifact failure.zip
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-artifacts:
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-<!DOCTYPE html>
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-<html lang="en">
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-        
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-        <meta name="author" content="Guangchuang Yu">
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-            <a class="navbar-brand" href=".">ggtree</a>
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-            
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-                <!-- Main navigation -->
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-                <ul class="nav navbar-nav">
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-                
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-                    <li >
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-                        <a href=".">Home</a>
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-                        <a href="documentation/">Documentation</a>
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-                <li>
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-                    <a href="#" data-toggle="modal" data-target="#mkdocs_search_modal">
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-                        <i class="fa fa-search"></i> Search
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-                    </a>
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-                </li>
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-                
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-                    <li class="disabled">
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-                        <a rel="next" >
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-                            <i class="fa fa-arrow-left"></i> Previous
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-                    <li class="disabled">
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-                        <a rel="prev" >
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-        <h1 id="404-page-not-found" style="text-align: center">404</h1>
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-        <p style="text-align: center"><strong>Page not found</strong></p>
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-        <footer class="col-md-12">
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-            <hr>
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-                <p>Copyright &copy; 2016 <a href="https://guangchuangyu.github.io">Guangchuang Yu</a>.</p>
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-            <p>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</p>
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-                    <div class="modal-header">
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-                        <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">&times;</span><span class="sr-only">Close</span></button>
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-                        <h4 class="modal-title" id="exampleModalLabel">Search</h4>
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-                        <p>
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-                            From here you can search these documents. Enter
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-                                <input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query">
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-            })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
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-
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-            ga('create', 'UA-77901140-1', 'guangchuangyu.github.io');
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-            ga('send', 'pageview');
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-        </script>
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-        
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-    </head>
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-    <body>
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-        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
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-    <div class="container">
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-            <!-- Expander button -->
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-                <span class="icon-bar"></span>
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-                <span class="icon-bar"></span>
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-            <!-- Main navigation -->
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-            <ul class="nav navbar-nav">
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-        <meta name="viewport" content="width=device-width, initial-scale=1.0">
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-        {% if page_description %}<meta name="description" content="{{ page_description }}">{% endif %}
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-        {% if site_author %}<meta name="author" content="{{ site_author }}">{% endif %}
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-        {% if canonical_url %}<link rel="canonical" href="{{ canonical_url }}">{% endif %}
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-	<title>{% if page_title %}{{ page_title }} - {% endif %}{{ site_name }}</title>
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-        <link href="{{ base_url }}/css/bootstrap-custom.min.css" rel="stylesheet">
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