guangchuang yu authored on 11/10/2016 02:07:36
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@@ -7,11 +7,4 @@ vignettes/.DS_Store
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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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-mkdocs
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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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+
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+alldocs: rd readme mkdocs
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+
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+rd:
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+	Rscript -e 'roxygen2::roxygenise(".")'
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+
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+readme:
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+	Rscript -e 'rmarkdown::render("README.Rmd")'
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+
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+build:
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+	cd ..;\
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+	R CMD build $(PKGSRC)
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+
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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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+
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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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+
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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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+
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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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+
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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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+
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+clean:
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+	cd ..;\
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+	$(RM) -r $(PKGNAME).Rcheck/
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+
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+site: mkdocs
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+
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+mkdocs: mdfiles
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+	cd mkdocs;\
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+	mkdocs build;\
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+	cd ../docs;\
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+	rm -rf fonts;\
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+	rm -rf css/font-awesome*
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+
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+mdfiles:
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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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+
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+
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+svnignore:
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+	svn propset svn:ignore -F .svnignore .
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+
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+svncommit:
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+	git checkout devel;\
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+	git svn rebase;\
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+	git merge master --log;\
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+	git svn dcommit;\
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+	git checkout master;\
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+	git merge devel
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+---
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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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+
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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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+
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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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+
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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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+
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+
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+
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+
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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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+
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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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+
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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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+
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+test_script:
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+  - travis-tool.sh run_tests
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+
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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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+
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+artifacts:
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+  - path: '*.Rcheck\**\*.log'
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+    name: Logs
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+
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+  - path: '*.Rcheck\**\*.out'
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+    name: Logs
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+
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+  - path: '*.Rcheck\**\*.fail'
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+    name: Logs
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+
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+  - path: '*.Rcheck\**\*.Rout'
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+    name: Logs
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+
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+  - path: '\*_*.tar.gz'
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+    name: Linux Package
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+
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+  - path: '\*_*.zip'
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+    name: Windows Package
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+<!DOCTYPE html>
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+<html lang="en">
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+    <head>
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+        <meta charset="utf-8">
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+        <meta http-equiv="X-UA-Compatible" content="IE=edge">
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+        <meta name="viewport" content="width=device-width, initial-scale=1.0">
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+        
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+        <meta name="author" content="Guangchuang Yu">
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+        <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/ChIPseeker/">
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+        <link rel="shortcut icon" href="../img/favicon.ico">
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+
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+	<title>ChIPseeker - ggtree</title>
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+
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+        <link href="../css/bootstrap-custom.min.css" rel="stylesheet">
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+        <link href="../css/font-awesome-4.0.3.css" rel="stylesheet">
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+        <link rel="stylesheet" href="../css/highlight.css">
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+        <link href="../css/base.css" rel="stylesheet">
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+
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+        <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
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+        <!--[if lt IE 9]>
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+            <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>
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+            <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script>
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+        <![endif]-->
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+
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+        
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+        <script>
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+            (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
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+            (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
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+            m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
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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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+
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+    <body>
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+
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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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+
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+        <!-- Collapsed navigation -->
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+        <div class="navbar-header">
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+            <!-- Expander button -->
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+            <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
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+                <span class="sr-only">Toggle navigation</span>
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+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
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+                <span class="icon-bar"></span>
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+            </button>
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+
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+            <!-- Main title -->
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+            <a class="navbar-brand" href="..">ggtree</a>
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+        </div>
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+
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+        <!-- Expanded navigation -->
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+        <div class="navbar-collapse collapse">
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+            <!-- Main navigation -->
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+            <ul class="nav navbar-nav">
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+            
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+            
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+                <li >
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+                    <a href="..">Home</a>
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+                </li>
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+            
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+            
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+            
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+                <li >
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+                    <a href="../documentation/">Documentation</a>
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+                </li>
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+            
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+            
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+            
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+                <li >
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+                    <a href="../faq/">FAQ</a>
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+                </li>
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+            
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+            
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+            
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+                <li >
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+                    <a href="../featuredArticles/">Featured Articles</a>
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+                </li>
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+            
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+            
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+            
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+                <li class="dropdown active">
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+                    <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a>
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+                    <ul class="dropdown-menu">
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+                    
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+                        
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+<li class="active">
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+    <a href="./">ChIPseeker</a>
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+</li>
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+
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+                    
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+                        
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+<li >
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+    <a href="../clusterProfiler/">clusterProfiler</a>
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+</li>
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+
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+                    
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+                        
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+<li >
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+    <a href="../DOSE/">DOSE</a>
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+</li>
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+
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+                    
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+                        
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+<li >
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+    <a href="../ggtree/">ggtree</a>
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+</li>
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+
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+                    
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+                        
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+<li >
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+    <a href="../GOSemSim/">GOSemSim</a>
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+</li>
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+
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+                    
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+                        
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+<li >
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+    <a href="../ReactomePA/">ReactomePA</a>
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+</li>
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+
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+                    
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+                    </ul>
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+                </li>
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+            
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+            
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+            </ul>
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+
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+            <!-- Search, Navigation and Repo links -->
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+            <ul class="nav navbar-nav navbar-right">
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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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+                <li >
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+                    <a rel="next" href="../featuredArticles/">
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+                        <i class="fa fa-arrow-left"></i> Previous
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+                    </a>
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+                </li>
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+                <li >
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+                    <a rel="prev" href="../clusterProfiler/">
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+                        Next <i class="fa fa-arrow-right"></i>
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+                    </a>
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+                </li>
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+                
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+                <li>
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+                    <a href="https://github.com/GuangchuangYu/ggtree">
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+                        
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+                            <i class="fa fa-github"></i>
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+                        
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+                        GitHub
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+                    </a>
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+                </li>
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+                
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+            </ul>
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+        </div>
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+    </div>
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+</div>
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+
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+        <div class="container">
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+            <div class="col-md-3"><div class="bs-sidebar hidden-print affix well" role="complementary">
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+    <ul class="nav bs-sidenav">
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+    
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+    </ul>
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+</div></div>
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+            <div class="col-md-9" role="main">
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+
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+<p><meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/ChIPseeker" /></p></div>
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+        </div>
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+
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+        <footer class="col-md-12">
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+            <hr>
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+            
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+                <center>Copyright &copy; 2016 <a href="https://guangchuangyu.github.io">Guangchuang Yu</a>.<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div></center>
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+            
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+            <center>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</center>
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+        </footer>
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+
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+        <script src="../js/jquery-1.10.2.min.js"></script>
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+        <script src="../js/bootstrap-3.0.3.min.js"></script>
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+        <script src="../js/highlight.pack.js"></script>
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+        <script>var base_url = '..';</script>
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+        <script data-main="../mkdocs/js/search.js" src="../mkdocs/js/require.js"></script>
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+        <script src="../js/base.js"></script>
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+
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+        <div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true">
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+            <div class="modal-dialog">
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+                <div class="modal-content">
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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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+                    </div>
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+                    <div class="modal-body">
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+                        <p>
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+                            From here you can search these documents. Enter
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+                            your search terms below.
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+                        </p>
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+                        <form role="form">
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+                            <div class="form-group">
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+                                <input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query">
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+                            </div>
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+                        </form>
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+                        <div id="mkdocs-search-results"></div>
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+                    <div class="modal-footer">
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+                    </div>
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+                </div>
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+        </div>
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+    </body>
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+</html>
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+<!DOCTYPE html>
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+<html lang="en">
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+    <head>
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+        <meta charset="utf-8">
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+        <meta http-equiv="X-UA-Compatible" content="IE=edge">
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+        <meta name="viewport" content="width=device-width, initial-scale=1.0">
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+        
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+        <meta name="author" content="Guangchuang Yu">
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+        <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/DOSE/">
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+        <link rel="shortcut icon" href="../img/favicon.ico">
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+
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+	<title>DOSE - ggtree</title>
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+
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+        <link href="../css/bootstrap-custom.min.css" rel="stylesheet">
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+        <link href="../css/font-awesome-4.0.3.css" rel="stylesheet">
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+        <link rel="stylesheet" href="../css/highlight.css">
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+        <link href="../css/base.css" rel="stylesheet">
18
+
19
+        <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
20
+        <!--[if lt IE 9]>
21
+            <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>
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+            <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script>
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+        <![endif]-->
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+
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+        
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+        <script>
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+            (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
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+            (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
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+            m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
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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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+
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+    <body>
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+
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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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+    <a href="../clusterProfiler/">clusterProfiler</a>
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+                    
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+            
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+                <center>Copyright &copy; 2016 <a href="https://guangchuangyu.github.io">Guangchuang Yu</a>.<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div></center>
180
+            
181
+            <center>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</center>
182
+        </footer>
183
+
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+        <script src="../js/jquery-1.10.2.min.js"></script>
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+        <script src="../js/bootstrap-3.0.3.min.js"></script>
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+        <script src="../js/highlight.pack.js"></script>
187
+        <script>var base_url = '..';</script>
188
+        <script data-main="../mkdocs/js/search.js" src="../mkdocs/js/require.js"></script>
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+        <script src="../js/base.js"></script>
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+
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+        <div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true">
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+            <div class="modal-dialog">
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+                <div class="modal-content">
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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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+                    </div>
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+                    <div class="modal-body">
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+                        <p>
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+                            From here you can search these documents. Enter
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+                            your search terms below.
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+                        </p>
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+                        <form role="form">
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+                            <div class="form-group">
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+                                <input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query">
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+                            </div>
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+                        </form>
208
+                        <div id="mkdocs-search-results"></div>
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+                    </div>
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+                    <div class="modal-footer">
211
+                    </div>
212
+                </div>
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+            </div>
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+        </div>
215
+    </body>
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+</html>
0 217
\ No newline at end of file
1 218
new file mode 100644
... ...
@@ -0,0 +1,94 @@
1
+<!DOCTYPE html>
2
+<html lang="en">
3
+    <head>
4
+        <meta charset="utf-8">
5
+        <meta http-equiv="X-UA-Compatible" content="IE=edge">
6
+        <meta name="viewport" content="width=device-width, initial-scale=1.0">
7
+        {% if page_description %}<meta name="description" content="{{ page_description }}">{% endif %}
8
+        {% if site_author %}<meta name="author" content="{{ site_author }}">{% endif %}
9
+        {% if canonical_url %}<link rel="canonical" href="{{ canonical_url }}">{% endif %}
10
+        {% if favicon %}<link rel="shortcut icon" href="{{ favicon }}">
11
+        {% else %}<link rel="shortcut icon" href="{{ base_url }}/img/favicon.ico">{% endif %}
12
+
13
+	<title>{% if page_title %}{{ page_title }} - {% endif %}{{ site_name }}</title>
14
+
15
+        <link href="{{ base_url }}/css/bootstrap-custom.min.css" rel="stylesheet">
16
+        <link href="{{ base_url }}/css/font-awesome-4.0.3.css" rel="stylesheet">
17
+        <link rel="stylesheet" href="{{ base_url }}/css/highlight.css">
18
+        <link href="{{ base_url }}/css/base.css" rel="stylesheet">
19
+        {%- for path in extra_css %}
20
+        <link href="{{ path }}" rel="stylesheet">
21
+        {%- endfor %}
22
+
23
+        <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
24
+        <!--[if lt IE 9]>
25
+            <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>
26
+            <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script>
27
+        <![endif]-->
28
+
29
+        {% if google_analytics %}
30
+        <script>
31
+            (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
32
+            (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
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+            m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
34
+            })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
35
+
36
+            ga('create', '{{ google_analytics[0] }}', '{{ google_analytics[1] }}');
37
+            ga('send', 'pageview');
38
+        </script>
39
+        {% endif %}
40
+    </head>
41
+
42
+    <body>
43
+
44
+        {% include "nav.html" %}
45
+
46
+        <div class="container">
47
+            <div class="col-md-3">{% include "toc.html" %}</div>
48
+            <div class="col-md-9" role="main">{% include "content.html" %}</div>
49
+        </div>
50
+
51
+        <footer class="col-md-12">
52
+            <hr>
53
+            {% if copyright %}
54
+                <center>{{ copyright }}</center>
55
+            {% endif %}
56
+            <center>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</center>
57
+        </footer>
58
+
59
+        <script src="{{ base_url }}/js/jquery-1.10.2.min.js"></script>
60
+        <script src="{{ base_url }}/js/bootstrap-3.0.3.min.js"></script>
61
+        <script src="{{ base_url }}/js/highlight.pack.js"></script>
62
+        <script>var base_url = '{{ base_url }}';</script>
63
+        <script data-main="{{ base_url }}/mkdocs/js/search.js" src="{{ base_url }}/mkdocs/js/require.js"></script>
64
+        <script src="{{ base_url }}/js/base.js"></script>
65
+        {%- for path in extra_javascript %}
66
+        <script src="{{ path }}"></script>
67
+        {%- endfor %}
68
+
69
+        <div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true">
70
+            <div class="modal-dialog">
71
+                <div class="modal-content">
72
+                    <div class="modal-header">
73
+                        <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">&times;</span><span class="sr-only">Close</span></button>
74
+                        <h4 class="modal-title" id="exampleModalLabel">Search</h4>
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+                    </div>
76
+                    <div class="modal-body">
77
+                        <p>
78
+                            From here you can search these documents. Enter
79
+                            your search terms below.
80
+                        </p>
81
+                        <form role="form">
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+                            <div class="form-group">
83
+                                <input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query">
84
+                            </div>
85
+                        </form>
86
+                        <div id="mkdocs-search-results"></div>
87
+                    </div>
88
+                    <div class="modal-footer">
89
+                    </div>
90
+                </div>
91
+            </div>
92
+        </div>
93
+    </body>
94
+</html>
0 95
new file mode 100644
... ...
@@ -0,0 +1,216 @@
1
+<!DOCTYPE html>
2
+<html lang="en">
3
+    <head>
4
+        <meta charset="utf-8">
5
+        <meta http-equiv="X-UA-Compatible" content="IE=edge">
6
+        <meta name="viewport" content="width=device-width, initial-scale=1.0">
7
+        
8
+        <meta name="author" content="Guangchuang Yu">
9
+        <link rel="canonical" href="https://guangchuangyu.github.io/ggtree/clusterProfiler/">
10
+        <link rel="shortcut icon" href="../img/favicon.ico">
11
+
12
+	<title>clusterProfiler - ggtree</title>
13
+
14
+        <link href="../css/bootstrap-custom.min.css" rel="stylesheet">
15
+        <link href="../css/font-awesome-4.0.3.css" rel="stylesheet">
16
+        <link rel="stylesheet" href="../css/highlight.css">
17
+        <link href="../css/base.css" rel="stylesheet">
18
+
19
+        <!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
20
+        <!--[if lt IE 9]>
21
+            <script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>
22
+            <script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script>
23
+        <![endif]-->
24
+
25
+        
26
+        <script>
27
+            (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
28
+            (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
29
+            m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
30
+            })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
31
+
32
+            ga('create', 'UA-77901140-1', 'guangchuangyu.github.io');
33
+            ga('send', 'pageview');
34
+        </script>
35
+        
36
+    </head>
37
+
38
+    <body>
39
+
40
+        <div class="navbar navbar-default navbar-fixed-top" role="navigation">
41
+    <div class="container">
42
+
43
+        <!-- Collapsed navigation -->
44
+        <div class="navbar-header">
45
+            <!-- Expander button -->
46
+            <button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
47
+                <span class="sr-only">Toggle navigation</span>
48
+                <span class="icon-bar"></span>
49
+                <span class="icon-bar"></span>
50
+                <span class="icon-bar"></span>
51
+            </button>
52
+
53
+            <!-- Main title -->
54
+            <a class="navbar-brand" href="..">ggtree</a>
55
+        </div>
56
+
57
+        <!-- Expanded navigation -->
58
+        <div class="navbar-collapse collapse">
59
+            <!-- Main navigation -->
60
+            <ul class="nav navbar-nav">
61
+            
62
+            
63
+                <li >
64
+                    <a href="..">Home</a>
65
+                </li>
66
+            
67
+            
68
+            
69
+                <li >
70
+                    <a href="../documentation/">Documentation</a>
71
+                </li>
72
+            
73
+            
74
+            
75
+                <li >
76
+                    <a href="../faq/">FAQ</a>
77
+                </li>
78
+            
79
+            
80
+            
81
+                <li >
82
+                    <a href="../featuredArticles/">Featured Articles</a>
83
+                </li>
84
+            
85
+            
86
+            
87
+                <li class="dropdown active">
88
+                    <a href="#" class="dropdown-toggle" data-toggle="dropdown">My Software <b class="caret"></b></a>
89
+                    <ul class="dropdown-menu">
90
+                    
91
+                        
92
+<li >
93
+    <a href="../ChIPseeker/">ChIPseeker</a>
94
+</li>
95
+
96
+                    
97
+                        
98
+<li class="active">
99
+    <a href="./">clusterProfiler</a>
100
+</li>
101
+
102
+                    
103
+                        
104
+<li >
105
+    <a href="../DOSE/">DOSE</a>
106
+</li>
107
+
108
+                    
109
+                        
110
+<li >
111
+    <a href="../ggtree/">ggtree</a>
112
+</li>
113
+
114
+                    
115
+                        
116
+<li >
117
+    <a href="../GOSemSim/">GOSemSim</a>
118
+</li>
119
+
120
+                    
121
+                        
122
+<li >
123
+    <a href="../ReactomePA/">ReactomePA</a>
124
+</li>
125
+
126
+                    
127
+                    </ul>
128
+                </li>
129
+            
130
+            
131
+            </ul>
132
+
133
+            <!-- Search, Navigation and Repo links -->
134
+            <ul class="nav navbar-nav navbar-right">
135
+                <li>
136
+                    <a href="#" data-toggle="modal" data-target="#mkdocs_search_modal">
137
+                        <i class="fa fa-search"></i> Search
138
+                    </a>
139
+                </li>
140
+                <li >
141
+                    <a rel="next" href="../ChIPseeker/">
142
+                        <i class="fa fa-arrow-left"></i> Previous
143
+                    </a>
144
+                </li>
145
+                <li >
146
+                    <a rel="prev" href="../DOSE/">
147
+                        Next <i class="fa fa-arrow-right"></i>
148
+                    </a>
149
+                </li>
150
+                
151
+                <li>
152
+                    <a href="https://github.com/GuangchuangYu/ggtree">
153
+                        
154
+                            <i class="fa fa-github"></i>
155
+                        
156
+                        GitHub
157
+                    </a>
158
+                </li>
159
+                
160
+            </ul>
161
+        </div>
162
+    </div>
163
+</div>
164
+
165
+        <div class="container">
166
+            <div class="col-md-3"><div class="bs-sidebar hidden-print affix well" role="complementary">
167
+    <ul class="nav bs-sidenav">
168
+    
169
+    </ul>
170
+</div></div>
171
+            <div class="col-md-9" role="main">
172
+
173
+<p><meta http-equiv="refresh" content="0; url=https://guangchuangyu.github.io/clusterProfiler" /></p></div>
174
+        </div>
175
+
176
+        <footer class="col-md-12">
177
+            <hr>
178
+            
179
+                <center>Copyright &copy; 2016 <a href="https://guangchuangyu.github.io">Guangchuang Yu</a>.<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&amp;m=0&amp;c=ff0000&amp;cr1=ffffff&amp;sx=0" async="async"></script></div></center>
180
+            
181
+            <center>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</center>
182
+        </footer>
183
+
184
+        <script src="../js/jquery-1.10.2.min.js"></script>
185
+        <script src="../js/bootstrap-3.0.3.min.js"></script>
186
+        <script src="../js/highlight.pack.js"></script>
187
+        <script>var base_url = '..';</script>
188
+        <script data-main="../mkdocs/js/search.js" src="../mkdocs/js/require.js"></script>
189
+        <script src="../js/base.js"></script>
190
+
191
+        <div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true">
192
+            <div class="modal-dialog">
193
+                <div class="modal-content">
194
+                    <div class="modal-header">
195
+                        <button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">&times;</span><span class="sr-only">Close</span></button>
196
+                        <h4 class="modal-title" id="exampleModalLabel">Search</h4>
197
+                    </div>
198
+                    <div class="modal-body">
199
+                        <p>
200
+                            From here you can search these documents. Enter
201
+                            your search terms below.
202
+                        </p>
203
+                        <form role="form">
204
+                            <div class="form-group">
205
+                                <input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query">
206
+                            </div>
207
+                        </form>
208
+                        <div id="mkdocs-search-results"></div>
209
+                    </div>
210
+                    <div class="modal-footer">
211
+                    </div>
212
+                </div>
213
+            </div>
214
+        </div>
215
+    </body>
216
+</html>
0 217
\ No newline at end of file
1 218
new file mode 100644
... ...
@@ -0,0 +1,9 @@
1
+{% if meta.source %}
2
+<div class="source-links">
3
+{% for filename in meta.source %}
4
+    <span class="label label-primary">{{ filename }}</span>
5
+{% endfor %}
6
+</div>
7
+{% endif %}
8
+
9
+{{ content }}
0 10
new file mode 100644
... ...
@@ -0,0 +1,155 @@
1
+body {
2
+    padding-top: 70px;
3
+}
4
+
5
+h1[id]:before, h2[id]:before, h3[id]:before, h4[id]:before, h5[id]:before, h6[id]:before {
6
+    content: "";
7
+    display: block;
8
+    margin-top: -75px;
9
+    height: 75px;
10
+}
11
+
12
+ul.nav li.main {
13
+    font-weight: bold;
14
+}
15
+
16
+div.col-md-3 {
17
+    padding-left: 0;
18
+}
19
+
20
+div.col-md-9 {
21
+    padding-bottom: 100px;
22
+}
23
+
24
+div.source-links {
25
+    float: right;
26
+}
27
+
28
+div.col-md-9 img {
29
+  max-width: 100%;
30
+}
31
+
32
+/*
33
+ * Side navigation
34
+ *
35
+ * Scrollspy and affixed enhanced navigation to highlight sections and secondary
36
+ * sections of docs content.
37
+ */
38
+
39
+/* By default it's not affixed in mobile views, so undo that */
40
+.bs-sidebar.affix {
41
+    position: static;
42
+}
43
+
44
+.bs-sidebar.well {
45
+    padding: 0;
46
+}
47
+
48
+/* First level of nav */
49
+.bs-sidenav {
50
+    margin-top: 30px;
51
+    margin-bottom: 30px;
52
+    padding-top:    10px;
53
+    padding-bottom: 10px;
54
+    border-radius: 5px;
55
+}
56
+
57
+/* All levels of nav */
58
+.bs-sidebar .nav > li > a {
59
+    display: block;
60
+    padding: 5px 20px;
61
+    z-index: 1;
62
+}
63
+.bs-sidebar .nav > li > a:hover,
64
+.bs-sidebar .nav > li > a:focus {
65
+    text-decoration: none;
66
+    border-right: 1px solid;
67
+}
68
+.bs-sidebar .nav > .active > a,
69
+.bs-sidebar .nav > .active:hover > a,
70
+.bs-sidebar .nav > .active:focus > a {
71
+    font-weight: bold;
72
+    background-color: transparent;
73
+    border-right: 1px solid;
74
+}
75
+
76
+/* Nav: second level (shown on .active) */
77
+.bs-sidebar .nav .nav {
78
+    display: none; /* Hide by default, but at >768px, show it */
79
+    margin-bottom: 8px;
80
+}
81
+.bs-sidebar .nav .nav > li > a {
82
+    padding-top:    3px;
83
+    padding-bottom: 3px;
84
+    padding-left: 30px;
85
+    font-size: 90%;
86
+}
87
+
88
+/* Show and affix the side nav when space allows it */
89
+@media (min-width: 992px) {
90
+    .bs-sidebar .nav > .active > ul {
91
+        display: block;
92
+    }
93
+    /* Widen the fixed sidebar */
94
+    .bs-sidebar.affix,
95
+    .bs-sidebar.affix-bottom {
96
+        width: 213px;
97
+    }
98
+    .bs-sidebar.affix {
99
+        position: fixed; /* Undo the static from mobile first approach */
100
+        top: 80px;
101
+    }
102
+    .bs-sidebar.affix-bottom {
103
+        position: absolute; /* Undo the static from mobile first approach */
104
+    }
105
+    .bs-sidebar.affix-bottom .bs-sidenav,
106
+    .bs-sidebar.affix .bs-sidenav {
107
+        margin-top: 0;
108
+        margin-bottom: 0;
109
+    }
110
+}
111
+@media (min-width: 1200px) {
112
+    /* Widen the fixed sidebar again */
113
+    .bs-sidebar.affix-bottom,
114
+    .bs-sidebar.affix {
115
+        width: 263px;
116
+    }
117
+}
118
+
119
+/* display submenu relative to parent*/
120
+.dropdown-submenu {
121
+    position: relative;
122
+}
123
+
124
+/* sub menu stlye */
125
+.dropdown-submenu>.dropdown-menu {
126
+    top: 0;
127
+    left: 100%;
128
+    margin-top: 0px;
129
+    margin-left: -1px;
130
+}
131
+
132
+/* display sub menu on hover*/
133
+.dropdown-submenu:hover>.dropdown-menu {
134
+    display: block;
135
+}
136
+
137
+/* little arrow */
138
+.dropdown-submenu>a:after {
139
+    display: block;
140
+    content: " ";
141
+    float: right;
142
+    width: 0;
143
+    height: 0;
144
+    border-color: transparent;
145
+    border-style: solid;
146
+    border-width: 5px 0 5px 5px;
147
+    border-left-color: #ccc;
148
+    margin-top: 5px;
149
+    margin-right: -10px;
150
+}
151
+
152
+/* little arrow of parent menu */
153
+.dropdown-submenu:hover>a:after {
154
+    border-left-color: #fff;
155
+}
0 156
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