Browse code

remove website

guangchuang yu authored on 05/03/2018 04:17:02
Showing135 changed files

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@@ -16,3 +16,4 @@ logo.png
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 ggtree_sticker.R
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 site_src
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 ggtree.png
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+^CONDUCT\.md$
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new file mode 100644
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@@ -0,0 +1,25 @@
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+# Contributor Code of Conduct
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+
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+As contributors and maintainers of this project, we pledge to respect all people who 
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+contribute through reporting issues, posting feature requests, updating documentation,
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+submitting pull requests or patches, and other activities.
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+
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+We are committed to making participation in this project a harassment-free experience for
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+everyone, regardless of level of experience, gender, gender identity and expression,
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+sexual orientation, disability, personal appearance, body size, race, ethnicity, age, or religion.
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+
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+Examples of unacceptable behavior by participants include the use of sexual language or
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+imagery, derogatory comments or personal attacks, trolling, public or private harassment,
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+insults, or other unprofessional conduct.
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+
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+Project maintainers have the right and responsibility to remove, edit, or reject comments,
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+commits, code, wiki edits, issues, and other contributions that are not aligned to this 
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+Code of Conduct. Project maintainers who do not follow the Code of Conduct may be removed 
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+from the project team.
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+
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+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by 
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+opening an issue or contacting one or more of the project maintainers.
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+
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+This Code of Conduct is adapted from the Contributor Covenant 
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+(http:contributor-covenant.org), version 1.0.0, available at 
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+http://contributor-covenant.org/version/1/0/0/
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@@ -4,7 +4,7 @@ PKGSRC  := $(shell basename `pwd`)
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 all: rd check clean
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-alldocs: site rd readme
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+alldocs: rd readme
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 rd:
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 	Rscript -e 'library(methods); devtools::document()'
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@@ -49,25 +49,6 @@ clean:
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 	cd ..;\
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 	$(RM) -r $(PKGNAME).Rcheck/
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-site:
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-	cd site_src;\
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-	ln -s ../../software/themes themes;\
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-	Rscript -e 'blogdown::build_site()';\
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-	rm themes;\
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-	cd ..
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-
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-vignette:
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-	cd site_src/vignettes;\
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-	Rscript -e 'ff = list.files(pattern=".R|rmd"); sapply(ff, function(f) rmarkdown::render(f))';\
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-	mv *html ../../docs/vignettes/
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-
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-preview:
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-	cd site_src;\
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-	ln -s ../../software/themes themes;\
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-	Rscript -e 'blogdown::serve_site()';\
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-	rm themes;\
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-	cd ..
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-
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 gitmaintain:
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 	git gc --auto;\
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@@ -89,19 +70,6 @@ push:
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 	git push origin master
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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 'source("render.R")';\
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-# 	cd docs;\
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-# 	ln -f -s ../mysoftware/* ./
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-
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 # svnignore:
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 # 	svn propset svn:ignore -F .svnignore .
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@@ -81,4 +81,9 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali
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+## Contributing
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+
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+We welcome any contributions! By participating in this project you agree to
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+abide by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md).
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+
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@@ -38,3 +38,8 @@ Please cite the following article when using `ggtree`:
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 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-25396/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1211/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 <img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>
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+
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+Contributing
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+------------
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+
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+We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md).
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-<?xml version="1.0" encoding="utf-8" standalone="yes" ?>
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-<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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-  <channel>
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-    <title>Categories on ggtree</title>
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-    <link>https://guangchuangyu.github.io/ggtree/categories/</link>
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-    <description>Recent content in Categories on ggtree</description>
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-    <generator>Hugo -- gohugo.io</generator>
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-    <copyright>Released under the Artistic-2.0 license</copyright>
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-        <center><span class="zaln"><a href="https://guangchuangyu.github.io/2017/11/bmc-journal-protects-paper-of-plagiarism/" class="zb">Plea to against BMC</a></span></center>
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-        <center><span class="zaln"><a href="https://guangchuangyu.github.io/blog_images/pay_qrcode.png" class="zb">赞赏</a></span></center>
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-<div id="vignettes" class="section level2">
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-<h2><i class="fa fa-book"></i> Vignettes</h2>
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-<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtree.html">ggtree</a></li>
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-<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeImport.html">Tree Data Import</a></li>
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-<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeVisualization.html">Tree Visualization</a></li>
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-<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeAnnotation.html">Tree Annotation</a></li>
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-<h2><i class="fa fa-wordpress"></i> Blog posts</h2>
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-<h3><i class="fa fa-angle-double-right"></i> News and updates</h3>
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-<li><a href="https://guangchuangyu.github.io/2014/12/viewing-and-annotating-phylogenetic-tree-with-ggtree">viewing and annotating phylogenetic tree with ggtree</a></li>
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-<li><a href="https://guangchuangyu.github.io/2015/01/ggtree-in-bioconductor-3.1">ggtree in Bioconductor 3.1</a></li>
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-<li><a href="https://guangchuangyu.github.io/2015/04/bioc-31-news-of-my-bioc-packages">BioC 3.1: NEWS of my BioC packages</a></li>
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-<li><a href="https://guangchuangyu.github.io/2015/10/bioc-32-news-of-my-bioc-packages">BioC 3.2: NEWS of my BioC packages</a></li>
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-<li><a href="https://guangchuangyu.github.io/2015/12/news-of-ggtree">News of ggtree</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/05/bioc-33-news-of-my-bioc-packages/">BioC 3.3: NEWS of my BioC packages</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/10/bioc-34-news-of-my-bioc-packages">BioC 3.4: NEWS of my BioC packages</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/08/ggtree-paper-published">ggtree paper published</a></li>
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-<h3><i class="fa fa-angle-double-right"></i> Data manipulation</h3>
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-<li><a href="https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree">subsetting data in ggtree</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format">ggtree supports phylip tree format</a></li>
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-<li><a href="http://guangchuangyu.github.io/2017/01/convert-graphic-object-to-tree-object-using-treeio/">convert graphic object to tree object using treeio</a></li>
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-<h3><i class="fa fa-angle-double-right"></i> Tree visualization</h3>
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-<li><a href="https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/">ggtree - updating a tree view</a></li>
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-<li><a href="https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree">an example of drawing beast tree using ggtree</a></li>
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-<li><a href="http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/">Phylogenetic trees in R using ggtree</a></li>
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-<li><a href="https://phe-bioinformatics.github.io/blog/2017/06/14/ggtree_exploration">Growing a ggtree</a></li>
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-<li><a href="https://phe-bioinformatics.github.io/blog/2017/07/07/ggtree_part2">Growing a ggtree - part 2, adding tip shapes</a></li>
391
-<li><a href="https://aschuerch.github.io/posts/2017-04-24-blog-post-1">Drawing a tree with colored tips in R (ggtree)</a></li>
392
-</ul>
393
-</div>
394
-<div id="tree-annotation" class="section level3">
395
-<h3><i class="fa fa-angle-double-right"></i> Tree annotation</h3>
396
-<ul>
397
-<li><a href="https://guangchuangyu.github.io/2016/01/label-edge-number-in-ggtree">label edge number in ggtree</a></li>
398
-<li><a href="http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/">Edge coloring with user data</a></li>
399
-<li><a href="https://guangchuangyu.github.io/2015/08/subview">subview</a></li>
400
-<li><a href="https://guangchuangyu.github.io/2016/01/annotate-a-phylogenetic-tree-with-insets">Annotate a phylogenetic tree with insets</a></li>
401
-<li><a href="https://guangchuangyu.github.io/2015/08/ggtree-annotate-phylogenetic-tree-with-local-images">ggtree annotate phylogenetic tree with local images</a></li>
402
-<li><a href="https://guangchuangyu.github.io/2016/03/embed-images-in-ggplot2-via-subview-and-annotate-a-phylogenetic-tree-with-images-using-inset-function">embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function</a></li>
403
-<li><a href="https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree">identify method for ggtree</a></li>
404
-<li><a href="https://guangchuangyu.github.io/2016/10/facet_plot-a-general-solution-to-associate-data-with-phylogenetic-tree/">facet_plot: a general solution to associate data with phylogenetic tree</a></li>
405
-<li><a href="https://guangchuangyu.github.io/2016/11/align-genomic-features-with-phylogenetic-tree/">align genomic features with phylogenetic tree</a></li>
406
-<li><a href="https://stackoverflow.com/questions/45384281/ggjoy-facet-with-ggtree">ggjoy facet with ggtree</a></li>
407
-<li><a href="https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/">xlim_tree: set x axis limits for only Tree panel</a></li>
408
-<li><a href="https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/">add layer to specific panel of facet_plot output</a></li>
409
-<li><a href="https://rgriff23.github.io/2017/05/11/primate-phylogeny-ggtree.html">Enhanced annotation of a primate phylogeny with ggtree</a></li>
410
-</ul>
411
-</div>
412
-<div id="tree-manipulation" class="section level3">
413
-<h3><i class="fa fa-angle-double-right"></i> Tree manipulation</h3>
414
-<ul>
415
-<li><a href="https://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree">flip and rotate branches in ggtree</a></li>
416
-<li><a href="https://jean.manguy.eu/post/subtrees-as-triangles-with-ggtree/">Subtrees as triangles with ggtree</a></li>
417
-</ul>
418
-</div>
419
-<div id="application" class="section level3">
420
-<h3><i class="fa fa-angle-double-right"></i> Application</h3>
421
-<ul>
422
-<li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/">ggtree for microbiome data</a></li>
423
-<li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-outbreak-data/">ggtree for outbreak data</a></li>
424
-<li><a href="http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/">ggtree version of plotTree</a></li>
425
-<li><a href="https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree">reproducible logo generated by ggtree</a></li>
426
-</ul>
427
-</div>
428
-<div id="funny-stuff" class="section level3">
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-<h3><i class="fa fa-angle-double-right"></i> Funny stuff</h3>
430
-<ul>
431
-<li><a href="https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts">ggtree with funny fonts</a></li>
432
-<li><a href="https://guangchuangyu.github.io/2015/09/comic-phylogenetic-tree-with-ggtree-and-comicr">comic phylogenetic tree with ggtree and comicR</a></li>
433
-<li><a href="https://guangchuangyu.github.io/2015/12/use-emoji-font-in-r">use emoji font in R</a></li>
434
-</ul>
435
-</div>
436
-</div>
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-<div id="slides" class="section level2">
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-<h2><i class="fa fa-slideshare"></i> Slides</h2>
439
-<ul>
440
-<li><a href="https://guangchuangyu.github.io/presentation/2014-ggplot2/">Generating publication quality figures using R &amp; ggplot2</a></li>
441
-<li><a href="https://guangchuangyu.github.io/presentation/2016-ggtree-chinar/">ggtree for visualization and annotation of phylogenetic trees</a></li>
442
-</ul>
443
-</div>
444
-<div id="video" class="section level2">
445
-<h2><i class="fa fa-youtube-play"></i> Video</h2>
446
-<ul>
447
-<li><a href="https://www.youtube.com/watch?v=KcF8Ec38mzI">interactive clade highlighting</a></li>
448
-<li><a href="https://www.youtube.com/watch?v=lKNn4QlPO0E">interactive rotating clades</a></li>
449
-<li><a href="https://www.youtube.com/watch?v=SmcceRD_jxg">interactive clade labeling</a></li>
450
-<li><a href="https://youtu.be/tqspAXM0UQE">R语言包ggtree 进化树绘图</a></li>
451
-</ul>
452
-</div>
453
-<div id="workflow" class="section level2">
454
-<h2><i class="fa fa-gift"></i> Workflow</h2>
455
-<ul>
456
-<li><a href="https://rpubs.com/gutijosh9430/124817">recreate a tree from a publication (<strong>Bloom</strong> <em>et al</em>, <strong><em>Science</em></strong> 2010)</a></li>
457
-</ul>
458
-</div>
459
-<div id="workshop" class="section level2">
460
-<h2><i class="fa fa-users"></i> Workshop</h2>
461
-<ul>
462
-<li><a href="https://4va.github.io/biodatasci/r-ggtree.html">Visualizing and Annotating Phylogenetic Trees with R+ggtree</a></li>
463
-</ul>
464
-</div>
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-date: 2017-07-24T00:11:02+01:00
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-title: Documentation
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-weight: 10
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-
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-
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-
7
-<link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
8
-
9
-## <i class="fa fa-book"></i> Vignettes
10
-
11
-+ [ggtree](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtree.html)
12
-+ [Tree Data Import](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeImport.html)
13
-+ [Tree Visualization](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeVisualization.html)
14
-+ [Tree Annotation](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeAnnotation.html)
15
-+ [Tree Manipulation](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeManipulation.html)
16
-+ [Advance Tree Annotation](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/advanceTreeAnnotation.html)
17
-+ [ggtree utilities](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtreeUtilities.html)
18
-+ [Phylomoji](https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html)
19
-
20
-
21
-## <i class="fa fa-wordpress"></i> Blog posts
22
-
23
-### <i class="fa fa-angle-double-right"></i> News and updates
24
-
25
-+ [viewing and annotating phylogenetic tree with ggtree](https://guangchuangyu.github.io/2014/12/viewing-and-annotating-phylogenetic-tree-with-ggtree)
26
-+ [ggtree in Bioconductor 3.1](https://guangchuangyu.github.io/2015/01/ggtree-in-bioconductor-3.1)
27
-+ [BioC 3.1: NEWS of my BioC packages](https://guangchuangyu.github.io/2015/04/bioc-31-news-of-my-bioc-packages)
28
-+ [BioC 3.2: NEWS of my BioC packages](https://guangchuangyu.github.io/2015/10/bioc-32-news-of-my-bioc-packages)
29
-+ [News of ggtree](https://guangchuangyu.github.io/2015/12/news-of-ggtree)
30
-+ [BioC 3.3: NEWS of my BioC packages](https://guangchuangyu.github.io/2016/05/bioc-33-news-of-my-bioc-packages/)
31
-+ [BioC 3.4: NEWS of my BioC packages](https://guangchuangyu.github.io/2016/10/bioc-34-news-of-my-bioc-packages)
32
-+ [ggtree paper published](https://guangchuangyu.github.io/2016/08/ggtree-paper-published)
33
-
34
-### <i class="fa fa-angle-double-right"></i> Data manipulation
35
-
36
-+ [subsetting data in ggtree](https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree)
37
-+ [ggtree supports phylip tree format](https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format)
38
-+ [convert graphic object to tree object using treeio](http://guangchuangyu.github.io/2017/01/convert-graphic-object-to-tree-object-using-treeio/)
39
-
40
-### <i class="fa fa-angle-double-right"></i> Tree visualization
41
-
42
-+ [ggtree - updating a tree view](https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/)
43
-+ [an example of drawing beast tree using ggtree](https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree)
44
-+ [Phylogenetic trees in R using ggtree](http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/) <i class="fa fa-arrow-left"></i> The Molecular Ecologist
45
-+ [Growing a ggtree](https://phe-bioinformatics.github.io/blog/2017/06/14/ggtree_exploration)
46
-+ [Growing a ggtree - part 2, adding tip shapes](https://phe-bioinformatics.github.io/blog/2017/07/07/ggtree_part2)
47
-
48
-### <i class="fa fa-angle-double-right"></i> Tree annotation
49
-
50
-+ [label edge number in ggtree](https://guangchuangyu.github.io/2016/01/label-edge-number-in-ggtree)
51
-+ [Edge coloring with user data](http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/)
52
-+ [subview](https://guangchuangyu.github.io/2015/08/subview)
53
-+ [Annotate a phylogenetic tree with insets](https://guangchuangyu.github.io/2016/01/annotate-a-phylogenetic-tree-with-insets)
54
-+ [ggtree annotate phylogenetic tree with local images](https://guangchuangyu.github.io/2015/08/ggtree-annotate-phylogenetic-tree-with-local-images)
55
-+ [embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function](https://guangchuangyu.github.io/2016/03/embed-images-in-ggplot2-via-subview-and-annotate-a-phylogenetic-tree-with-images-using-inset-function)
56
-+ [identify method for ggtree](https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree)
57
-+ [facet_plot: a general solution to associate data with phylogenetic tree](https://guangchuangyu.github.io/2016/10/facet_plot-a-general-solution-to-associate-data-with-phylogenetic-tree/)
58
-+ [align genomic features with phylogenetic tree](https://guangchuangyu.github.io/2016/11/align-genomic-features-with-phylogenetic-tree/)
59
-+ [ggjoy facet with ggtree](https://stackoverflow.com/questions/45384281/ggjoy-facet-with-ggtree)
60
-+ [xlim_tree: set x axis limits for only Tree panel](https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/)
61
-+ [add layer to specific panel of facet_plot output](https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/)
62
-
63
-
64
-### <i class="fa fa-angle-double-right"></i> Tree manipulation
65
-
66
-+ [flip and rotate branches in ggtree](https://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree)
67
-
68
-### <i class="fa fa-angle-double-right"></i> Application
69
-
70
-+ [ggtree for microbiome data](https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/)
71
-+ [ggtree for outbreak data](https://guangchuangyu.github.io/2016/09/ggtree-for-outbreak-data/)
72
-+ [ggtree version of plotTree](http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/)
73
-+ [reproducible logo generated by ggtree](https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree)
74
-
75
-
76
-### <i class="fa fa-angle-double-right"></i> Funny stuff
77
-
78
-+ [ggtree with funny fonts](https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts)
79
-+ [comic phylogenetic tree with ggtree and comicR](https://guangchuangyu.github.io/2015/09/comic-phylogenetic-tree-with-ggtree-and-comicr)
80
-+ [use emoji font in R](https://guangchuangyu.github.io/2015/12/use-emoji-font-in-r)
81
-
82
-
83
-## <i class="fa fa-slideshare"></i> Slides
84
-
85
-+ [Generating publication quality figures using R & ggplot2](https://guangchuangyu.github.io/presentation/2014-ggplot2/)
86
-+ [ggtree for visualization and annotation of phylogenetic trees](https://guangchuangyu.github.io/presentation/2016-ggtree-chinar/)
87
-
88
-## <i class="fa fa-youtube-play"></i> Video
89
-
90
-+ [interactive clade highlighting](https://www.youtube.com/watch?v=KcF8Ec38mzI)
91
-+ [interactive rotating clades](https://www.youtube.com/watch?v=lKNn4QlPO0E)
92
-+ [interactive clade labeling](https://www.youtube.com/watch?v=SmcceRD_jxg)
93
-
94
-## <i class="fa fa-gift"></i> Workflow
95
-
96
-+ [recreate a tree from a publication (__Bloom__ *et al*, __*Science*__ 2010)](https://rpubs.com/gutijosh9430/124817)
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-      <description> Vignettes  ggtree Tree Data Import Tree Visualization Tree Annotation Tree Manipulation Advance Tree Annotation ggtree utilities Phylomoji    Blog posts  News and updates  viewing and annotating phylogenetic tree with ggtree ggtree in Bioconductor 3.1 BioC 3.1: NEWS of my BioC packages BioC 3.2: NEWS of my BioC packages News of ggtree BioC 3.3: NEWS of my BioC packages BioC 3.4: NEWS of my BioC packages ggtree paper published    Data manipulation  subsetting data in ggtree ggtree supports phylip tree format convert graphic object to tree object using treeio    Tree visualization  ggtree - updating a tree view an example of drawing beast tree using ggtree Phylogenetic trees in R using ggtree Growing a ggtree Growing a ggtree - part 2, adding tip shapes Drawing a tree with colored tips in R (ggtree)    Tree annotation  label edge number in ggtree Edge coloring with user data subview Annotate a phylogenetic tree with insets ggtree annotate phylogenetic tree with local images embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function identify method for ggtree facet_plot: a general solution to associate data with phylogenetic tree align genomic features with phylogenetic tree ggjoy facet with ggtree xlim_tree: set x axis limits for only Tree panel add layer to specific panel of facet_plot output Enhanced annotation of a primate phylogeny with ggtree    Tree manipulation  flip and rotate branches in ggtree Subtrees as triangles with ggtree    Application  ggtree for microbiome data ggtree for outbreak data ggtree version of plotTree reproducible logo generated by ggtree    Funny stuff  ggtree with funny fonts comic phylogenetic tree with ggtree and comicR use emoji font in R     Slides  Generating publication quality figures using R &amp;amp; ggplot2 ggtree for visualization and annotation of phylogenetic trees    Video  interactive clade highlighting interactive rotating clades interactive clade labeling R语言包ggtree 进化树绘图    Workflow  recreate a tree from a publication (Bloom et al, Science 2010)    Workshop  Visualizing and Annotating Phylogenetic Trees with R+ggtree   </description>
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-			<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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-<div id="installation" class="section level2">
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-<h2><i class="fa fa-download"></i> Installation</h2>
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-<h3><i class="fa fa-angle-double-right"></i> Could not find function</h3>
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-<p>If you got <a href="https://github.com/GuangchuangYu/ggtree/issues/12">this error</a>, please make sure you are using the latest R and <code>ggtree</code>.</p>
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-<p>Packages in Bioconductor, like <code>ggtree</code>, have different release policy compare to CRAN. There are two branches, release and devel, in parallel. Release branch is more stable and only document improvement and bug fixes will commit to it. New functions will only commit to <code>devel</code> branch.</p>
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-<p>Sometimes I may write blog post to introduce new functions which is not available in <code>release</code> branch, you need to install the <code>devel</code> version of <code>ggtree</code> in order to use these new functions.</p>
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-<p>You can download the <code>devel</code> version of <code>ggtree</code> from <a href="http://bioconductor.org/packages/devel/bioc/html/ggtree.html" class="uri">http://bioconductor.org/packages/devel/bioc/html/ggtree.html</a> and install it, or install the github version of <code>ggtree</code>.</p>
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-<p>This also applied to other of my packages, including <code>GOSemSim</code>, <code>DOSE</code>, <code>clusterProfiler</code>, <code>ReactomePA</code> and <code>ChIPseeker</code>. If you got the <code>could not find function</code> error, upgrade your installation to latest release. If the error still exists after upgrading to latest release, you need to install the devel version.</p>
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-<h2><i class="fa fa-check-square-o"></i> Basic R related</h2>
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-<h3><i class="fa fa-angle-double-right"></i> <code>system.file()</code></h3>
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-<p>If you are new to <code>R</code> and want to use <code>ggtree</code> for tree visualization, please do learn some basic <code>R</code> and <code>ggplot2</code>.</p>
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-<p>A very common issue is that users always copy-paste command without looking at the function’s behavior. <code>system.file()</code> was used in the <code>treeio</code> and <code>ggtree</code> vignettes to find files in the packages.</p>
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-<pre><code>system.file                package:base                R Documentation
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-Find Names of R System Files
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-Description:
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-     Finds the full file names of files in packages etc.
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-Usage:
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-     system.file(..., package = &quot;base&quot;, lib.loc = NULL,
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-                 mustWork = FALSE)</code></pre>
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-<p>For users who want to use <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/VsE22NnScdc/LHtJSEntDAAJ">their own files</a>, please just use relative or absolute file path (<em>e.g.</em> <code>f = &quot;your/folder/filename&quot;</code>).</p>
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-<h2><i class="fa fa-text-height"></i> Text &amp; Label</h2>
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-<div id="tip-label-truncated" class="section level3">
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-<h3><i class="fa fa-angle-double-right"></i> Tip label truncated</h3>
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-<p>ggplot2 can’t auto adjust xlim based on added text.</p>
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-<pre class="r"><code>library(ggtree)
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-## example tree from https://support.bioconductor.org/p/72398/
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-tree&lt;-read.tree(text=&quot;(Organism1.006G249400.1:0.03977,(Organism2.022118m:0.01337,(Organism3.J34265.1:0.00284,Organism4.G02633.1:0.00468)0.51:0.0104):0.02469);&quot;)
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-ggtree(tree) + geom_tiplab()</code></pre>
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-<p>This is because the units are in two different spaces (data and pixel). Users can use xlim to allocate more space for tip label.</p>
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-<pre class="r"><code>ggtree(tree) + geom_tiplab() + xlim(0, 0.06)</code></pre>
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-<div id="modify-tip-labels" class="section level3">
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-<h3><i class="fa fa-angle-double-right"></i> Modify (tip) labels</h3>
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-<p>This could be easily done via the <code>%&lt;+%</code> operator to attach the modified version of the labels and than use <code>geom_tiplab</code> to display the modified version.</p>
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-<pre><code>raxml_file &lt;- system.file(&quot;extdata/RAxML&quot;, &quot;RAxML_bipartitionsBranchLabels.H3&quot;, package=&quot;ggtree&quot;)
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-raxml &lt;- read.raxml(raxml_file)
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-lb = get.tree(raxml)$tip.label
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-d = data.frame(label=lb, label2 = paste(&quot;AA&quot;, substring(lb, 1, 5)))
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-ggtree(raxml) %&lt;+% d + geom_tiplab(aes(label=label2))</code></pre>
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-<p>see also <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/tFdFgCJ7gQA/tZ6phSgUDQAJ">1</a> and <a href="https://github.com/GuangchuangYu/ggtree/issues/106">2</a>.</p>
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-<div id="formatting-tip-labels" class="section level3">
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-<h3><i class="fa fa-angle-double-right"></i> Formatting (tip) labels</h3>
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-<p>If you want to format labels, you need to set <code>parse=TRUE</code> in <code>geom_text</code>/<code>geom_tiplab</code> and the <code>label</code> should be string that can be parsed into expression and displayed as described in <code>?plotmath</code>.</p>
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-<p>For example, the tiplabels contains two parts, species name and accession number and we want to display species name in <em>italic</em>, we can use command like this:</p>
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-<pre><code>ggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label=&#39;paste(italic(&quot;species name&quot;), &quot;accession number&quot;)&#39;, parse=T)</code></pre>
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-<p>Another example for formating all tip labels:</p>
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-<pre class="r"><code>ggtree(rtree(30)) + geom_tiplab(aes(label=paste0(&#39;bold(&#39;, label, &#39;)~italic(&#39;, node, &#39;)&#39;)), parse=TRUE)</code></pre>
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-<p>The <code>label</code> can be provided by a <code>data.frame</code> that contains related information of the taxa.</p>
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-<pre class="r"><code>tr &lt;- read.tree(text = &quot;((a,(b,c)),d);&quot;)
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-genus &lt;- c(&quot;Gorilla&quot;, &quot;Pan&quot;, &quot;Homo&quot;, &quot;Pongo&quot;)
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-species &lt;- c(&quot;gorilla&quot;, &quot;spp.&quot;, &quot;sapiens&quot;, &quot;pygmaeus&quot;)
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-geo &lt;- c(&quot;Africa&quot;, &quot;Africa&quot;, &quot;World&quot;, &quot;Asia&quot;)
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-d &lt;- data.frame(label = tr$tip.label, genus = genus,
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-                species = species, geo = geo)
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-ggtree(tr) %&lt;+% d + xlim(NA, 5) +
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-    geom_tiplab(aes(label=paste0(&#39;italic(&#39;, genus, &#39;)~bolditalic(&#39;, species, &#39;)~&#39;, geo)), parse=T)</code></pre>
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-<p>see also <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM" class="uri">https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM</a>.</p>
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-</div>
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-<div id="avoid-overlapping-text-labels" class="section level3">
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-<h3><i class="fa fa-angle-double-right"></i> Avoid overlapping text labels</h3>
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-<p>User can use <a href="https://cran.r-project.org/web/packages/ggrepel/">ggrepel</a> package to repel overlapping text labels.</p>
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-<p>For example:</p>
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-<pre class="r"><code>library(ggrepel)
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-library(ggtree)
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-raxml_file &lt;- system.file(&quot;extdata/RAxML&quot;, &quot;RAxML_bipartitionsBranchLabels.H3&quot;, package=&quot;ggtree&quot;)
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-raxml &lt;- read.raxml(raxml_file)
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-ggtree(raxml) + geom_label_repel(aes(label=bootstrap, fill=bootstrap))</code></pre>
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-<p>For details, please refer to <a href="https://cran.r-project.org/web/packages/ggrepel/vignettes/ggrepel.html">ggrepel usage examples</a>.</p>
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-</div>
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-<div id="bootstrap-values-from-newick-format" class="section level3">
432
-<h3><i class="fa fa-angle-double-right"></i> bootstrap values from newick format</h3>
433
-<p>It’s quite command to store <code>bootstrap</code> value as node label in <code>newick</code> format. Visualizing node label is easy using <code>geom_text2(aes(subset = !isTip, label=label))</code>.</p>
434
-<p>If you want to only display a subset of <code>bootstrap</code> (e.g. bootstrap &gt; 80), you can’t simply using <code>geom_text2(subset= (label &gt; 80), label=label)</code> since <code>label</code> is a character vector, which contains node label (bootstrap value) and tip label (taxa name). If we use <code>geom_text2(subset=(as.numeric(label) &gt; 80), label=label)</code>, it will also fail since <code>NAs</code> were introduced by coercion. We need to convert <code>NAs</code> to logical <code>FALSE</code>, this can be done by the following code:</p>
435
-<pre class="r"><code>nwk &lt;- system.file(&quot;extdata/RAxML&quot;,&quot;RAxML_bipartitions.H3&quot;, package=&#39;ggtree&#39;)
436
-tr &lt;- read.tree(nwk)
437
-ggtree(tr) + geom_text2(aes(label=label, subset = !is.na(as.numeric(label)) &amp; as.numeric(label) &gt; 80))</code></pre>
438
-<p>Another solution is converting the bootstrap value outside <code>ggtree</code> as I recommended in <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/hiRBjGaAfI0/Y-2zDpvtAwAJ">google group</a>.</p>
439
-<pre class="r"><code>q &lt;- ggtree(tr)
440
-d &lt;- q$data
441
-d &lt;- d[!d$isTip,]
442
-d$label &lt;- as.numeric(d$label)
443
-d &lt;- d[d$label &gt; 80,]
444
-
445
-q + geom_text(data=d, aes(label=label))</code></pre>
446
-<p><a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/ZeR8YZKIzq8/g5RCB_MiAQAJ">Here is another exammple</a> for multiple bootstrap support values.</p>
447
-</div>
448
-</div>
449
-<div id="aesthetic-mapping" class="section level2">
450
-<h2><i class="fa fa-map-marker"></i> <em>aesthetic</em> mapping</h2>
451
-<div id="inherit-aes" class="section level3">
452
-<h3><i class="fa fa-angle-double-right"></i> inherit <em>aes</em></h3>
453
-<pre class="r"><code>ggtree(rtree(30)) + geom_point()</code></pre>
454
-<p>For example, we can add symbolic points to nodes with <code>geom_point()</code> directly. The magic here is we don’t need to map <code>x</code> and <code>y</code> position of the points by providing <code>aes(x, y)</code> to <code>geom_point()</code> since it was already mapped by <code>ggtree</code> function and it serves as a global mapping for all layers.</p>
455
-<p>But what if we provide a <code>dataset</code> in a layer and the <code>dataset</code> doesn’t contain column of <code>x</code> and/or <code>y</code>, the layer function also try to map <code>x</code> and <code>y</code> and also others if you map them in <code>ggtree</code> function. As these variable is not available in your <code>dataset</code>, you will get the following error:</p>
456
-<pre><code>Error in eval(expr, envir, enclos) : object &#39;x&#39; not found</code></pre>
457
-<p>This can be fixed by using parameter <code>inherit.aes=FALSE</code> which will disable inheriting mapping from <code>ggtree</code> function.</p>
458
-</div>
459
-<div id="use-in-aes" class="section level3">
460
-<h3><i class="fa fa-angle-double-right"></i> use <code>$</code> in aes</h3>
461
-<p>NEVER DO THIS.</p>
462
-<p>see the explaination in the <a href="https://github.com/hadley/ggplot2-book/blob/master/layers.rmd#aesthetic-mappings-secaes">ggplot2 book 2ed</a>:</p>
463
-<blockquote>
464
-<p>Never refer to a variable with <code>$</code> (e.g., <code>diamonds$carat</code>) in <code>aes()</code>. This breaks containment, so that the plot no longer contains everything it needs, and causes problems if ggplot2 changes the order of the rows, as it does when facetting.</p>
465
-</blockquote>
466
-<p>see also <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/hViM6vRZF94/MsZT8qRgBwAJ">1</a> and <a href="https://github.com/GuangchuangYu/ggtree/issues/106">2</a>.</p>
467
-</div>
468
-</div>
469
-<div id="annotation" class="section level2">
470
-<h2><i class="fa fa-tree"></i> Annotation</h2>
471
-<div id="colouring-edges-by-user-data" class="section level3">
472
-<h3><i class="fa fa-angle-double-right"></i> colouring edges by user data</h3>
473
-<p>see my blog post: <a href="http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/">Edge coloring with user data</a> and also my answer on <a href="https://github.com/GuangchuangYu/ggtree/issues/76" class="uri">https://github.com/GuangchuangYu/ggtree/issues/76</a> and <a href="https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8" class="uri">https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8</a>.</p>
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-date: 2017-07-24T00:11:02+01:00
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-title: FAQ
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-weight: 20
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-
5
-
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-<link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
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-
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-
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-# <i class="fa fa-download"></i> Installation
10
-
11
-## <i class="fa fa-angle-double-right"></i> Could not find function
12
-
13
-If you got [this error](https://github.com/GuangchuangYu/ggtree/issues/12), please make sure you are using the latest R and `ggtree`.
14
-
15
-Packages in Bioconductor, like `ggtree`, have different release policy compare to CRAN. There are two branches, release and devel, in parallel. Release branch is more stable and only document improvement and bug fixes will commit to it. New functions will only commit to `devel` branch.
16
-
17
-Sometimes I may write blog post to introduce new functions which is not available in `release` branch, you need to install the `devel` version of `ggtree` in order to use these new functions.
18
-
19
-You can download the `devel` version of `ggtree` from [http://bioconductor.org/packages/devel/bioc/html/ggtree.html](http://bioconductor.org/packages/devel/bioc/html/ggtree.html) and install it, or install the github version of `ggtree`.
20
-
21
-This also applied to other of my packages, including `GOSemSim`, `DOSE`, `clusterProfiler`, `ReactomePA` and `ChIPseeker`. If you got the `could not find function` error, upgrade your installation to latest release. If the error still exists after upgrading to latest release, you need to install the devel version.
22
-
23
-
24
-# <i class="fa fa-text-height"></i> Text & Label
25
-
26
-## <i class="fa fa-angle-double-right"></i> Tip label truncated
27
-
28
-ggplot2 can't auto adjust xlim based on added text.
29
-
30
-```r
31
-library(ggtree)
32
-## example tree from https://support.bioconductor.org/p/72398/
33
-tree<-read.tree(text="(Organism1.006G249400.1:0.03977,(Organism2.022118m:0.01337,(Organism3.J34265.1:0.00284,Organism4.G02633.1:0.00468)0.51:0.0104):0.02469);")
34
-ggtree(tree) + geom_tiplab()
35
-```
36
-
37
-This is because the units are in two different spaces (data and pixel). Users can use xlim to allocate more space for tip label.
38
-
39
-```r
40
-ggtree(tree) + geom_tiplab() + xlim(0, 0.06)
41
-```
42
-
43
-## <i class="fa fa-angle-double-right"></i> Modify (tip) labels
44
-
45
-This could be easily done via the `%<+%` operator to attach the
46
-modified version of the labels and than use `geom_tiplab` to display
47
-the modified version.
48
-
49
-
50
-```
51
-raxml_file <- system.file("extdata/RAxML", "RAxML_bipartitionsBranchLabels.H3", package="ggtree")
52
-raxml <- read.raxml(raxml_file)
53
-
54
-lb = get.tree(raxml)$tip.label
55
-d = data.frame(label=lb, label2 = paste("AA", substring(lb, 1, 5)))
56
-ggtree(raxml) %<+% d + geom_tiplab(aes(label=label2))
57
-```
58
-
59
-see also
60
-[1](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/tFdFgCJ7gQA/tZ6phSgUDQAJ)
61
-and [2](https://github.com/GuangchuangYu/ggtree/issues/106).
62
-
63
-## <i class="fa fa-angle-double-right"></i> Formatting (tip) labels
64
-
65
-If you want to format labels, you need to set `parse=TRUE` in `geom_text`/`geom_tiplab` and the `label` should be string that can be parsed into expression and displayed as described in `?plotmath`.
66
-
67
-For example, the tiplabels contains two parts, species name and accession number and we want to display species name in _italic_, we can use command like this:
68
-
69
-```
70
-ggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label='paste(italic("species name"), "accession number")', parse=T)
71
-```
72
-
73
-
74
-Another example for formating all tip labels:
75
-
76
-```
77
-ggtree(rtree(30)) + geom_tiplab(aes(label=paste0('bold(', label, ')~italic(', node, ')')), parse=TRUE)
78
-```
79
-
80
-see
81
-also
82
-<https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM>.
83
-
84
-
85
-## <i class="fa fa-angle-double-right"></i> Avoid overlapping text labels
86
-
87
-User can use [ggrepel](https://cran.r-project.org/web/packages/ggrepel/) package to repel overlapping text labels.
88
-
89
-For example:
90
-
91
-```r
92
-library(ggrepel)
93
-library(ggtree)
94
-raxml_file <- system.file("extdata/RAxML", "RAxML_bipartitionsBranchLabels.H3", package="ggtree")
95
-raxml <- read.raxml(raxml_file)
96
-ggtree(raxml) + geom_label_repel(aes(label=bootstrap, fill=bootstrap))
97
-```
98
-
99
-For details, please refer to [ggrepel usage examples](https://cran.r-project.org/web/packages/ggrepel/vignettes/ggrepel.html).
100
-
101
-## <i class="fa fa-angle-double-right"></i> bootstrap values from newick format
102
-
103
-It's quite command to store `bootstrap` value as node label in `newick` format. Visualizing node label is easy using `geom_text2(aes(subset = !isTip, label=label))`.
104
-
105
-If you want to only display a subset of `bootstrap` (e.g. bootstrap > 80), you can't simply using `geom_text2(subset= (label > 80), label=label)` since `label` is a character vector, which contains node label (bootstrap value) and tip label (taxa name). If we use `geom_text2(subset=(as.numeric(label) > 80), label=label)`, it will also fail since `NAs` were introduced by coercion. We need to convert `NAs` to logical `FALSE`, this can be done by the following code:
106
-
107
-```r
108
-nwk <- system.file("extdata/RAxML","RAxML_bipartitions.H3", package='ggtree')
109
-tr <- read.tree(nwk)
110
-ggtree(tr) + geom_text2(aes(label=label, subset = !is.na(as.numeric(label)) & as.numeric(label) > 80))
111
-```
112
-
113
-Another solution is converting the bootstrap value outside `ggtree` as I recommended in [google group](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/hiRBjGaAfI0/Y-2zDpvtAwAJ).
114
-
115
-```r
116
-q <- ggtree(tr)
117
-d <- q$data
118
-d <- d[!d$isTip,]
119
-d$label <- as.numeric(d$label)
120
-d <- d[d$label > 80,]
121
-
122
-q + geom_text(data=d, aes(label=label))
123
-```
124
-
125
-
126
-# <i class="fa fa-map-marker"></i> _aesthetic_ mapping
127
-
128
-## <i class="fa fa-angle-double-right"></i> inherit _aes_
129
-
130
-```r
131
-ggtree(rtree(30)) + geom_point()
132
-```
133
-
134
-For example, we can add symbolic points to nodes with `geom_point()` directly.
135
-The magic here is we don't need to map `x` and `y` position of the points by providing `aes(x, y)` to `geom_point()` since it was already mapped by `ggtree` function and it serves as a global mapping for all layers.
136
-
137
-But what if we provide a `dataset` in a layer and the `dataset` doesn't contain column of `x` and/or `y`,
138
-the layer function also try to map `x` and `y` and also others if you map them in `ggtree` function.
139
-As these variable is not available in your `dataset`, you will get the following error:
140
-
141
-```
142
-Error in eval(expr, envir, enclos) : object 'x' not found
143
-```
144
-
145
-This can be fixed by using parameter `inherit.aes=FALSE` which will disable inheriting mapping from `ggtree` function.
146
-
147
-## <i class="fa fa-angle-double-right"></i> use `$` in aes
148
-
149
-NEVER DO THIS.
150
-
151
-see the explaination in the [ggplot2 book 2ed](https://github.com/hadley/ggplot2-book/blob/master/layers.rmd#aesthetic-mappings-secaes):
152
-
153
->Never refer to a variable with `$` (e.g., `diamonds$carat`) in `aes()`. This breaks containment, so that the plot no longer contains everything it needs, and causes problems if ggplot2 changes the order of the rows, as it does when facetting.
154
-
155
-see also
156
-[1](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/hViM6vRZF94/MsZT8qRgBwAJ)
157
-and [2](https://github.com/GuangchuangYu/ggtree/issues/106).
158
-
159
-
160
-# <i class="fa fa-tree"></i> Annotation
161
-
162
-## <i class="fa fa-angle-double-right"></i> colouring edges by user data
163
-
164
-see my blog post:
165
-[Edge coloring with user data](http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/)
166
-and also my answer on <https://github.com/GuangchuangYu/ggtree/issues/76>
167
-and <https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8>.
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-
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-    <title>Faqs on ggtree</title>
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-    <link>https://guangchuangyu.github.io/ggtree/faq/</link>
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-    <description>Recent content in Faqs on ggtree</description>
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-    <lastBuildDate>Mon, 24 Jul 2017 00:11:02 +0100</lastBuildDate>
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-      <title>FAQ</title>
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-      <link>https://guangchuangyu.github.io/ggtree/faq/</link>
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-      <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
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-      
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-      <guid>https://guangchuangyu.github.io/ggtree/faq/</guid>
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-      <description>Installation  Could not find function If you got this error, please make sure you are using the latest R and ggtree.
22
-Packages in Bioconductor, like ggtree, have different release policy compare to CRAN. There are two branches, release and devel, in parallel. Release branch is more stable and only document improvement and bug fixes will commit to it. New functions will only commit to devel branch.
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-Sometimes I may write blog post to introduce new functions which is not available in release branch, you need to install the devel version of ggtree in order to use these new functions.</description>
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