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GitHub - YuLab-SMU/ggtree: :christmas_tree:Visualization and annotation of phylogenetic trees

:christmas_tree:Visualization and annotation of phylogenetic trees - YuLab-SMU/ggtree

GitHub - YuLab-SMU/ggtree: :christmas_tree:Visualization and annotation of phylogenetic trees

GitHub - YuLab-SMU/ggtree: :christmas_tree:Visualization and annotation of phylogenetic trees

ggtree: an R package for visualization of phylogenetic trees with their annotation data

‘ggtree’ extends the ‘ggplot2’ plotting system which implemented the grammar of graphics. ‘ggtree’ is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.

:writing_hand: Authors

Guangchuang YU

School of Basic Medical Sciences, Southern Medical University

https://yulab-smu.top

If you use ggtree in published research, please cite the most appropriate paper(s) from this list:

S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan, G Yu. Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data. iMeta, 2022, 1(4):e56. doi: 10.1002/imt2.56
G Yu. Data Integration, Manipulation and Visualization of Phylogenetic Treess (1st edition). Chapman and Hall/CRC, 2022. doi: 10.1201/9781003279242
G Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics, 2020, 69:e96. doi: 10.1002/cpbi.96
- Source code and data to reproduce figures in the article
G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. doi: 10.1093/molbev/msy194
- Source code to produce Supplementary Material
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. 2017, 8(1):28-36. doi: 10.1111/2041-210X.12628

:sparkling_heart: Contributing

We welcome any contributions! By participating in this project you agree to abide by the terms outlined in the Contributor Code of Conduct.

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R wrapper for highcharts
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105
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Interactive JS Charts from R
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108
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109
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111
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116
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Contribute to vertica/DistributedR development by creating an account on GitHub.
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118
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120
:maple_leaf: Make waffle (square pie) charts in R
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Rcpp Bindings to C++ parser for TOML files. Contribute to eddelbuettel/rcpptoml development by creating an account on GitHub.
122
Neo4j Driver for R.
https://github.com/nicolewhite/Rneo4j
Neo4j Driver for R. Contribute to nicolewhite/RNeo4j development by creating an account on GitHub.
123
Tools for using fonts in R graphics
https://github.com/wch/extrafont
Tools for using fonts in R graphics. Contribute to wch/extrafont development by creating an account on GitHub.
124
Accelerating ggplot2
https://github.com/thomasp85/ggforce
Accelerating ggplot2. Contribute to thomasp85/ggforce development by creating an account on GitHub.
125
Easy interactive web applications with R
https://github.com/rstudio/shiny
Easy interactive web applications with R. Contribute to rstudio/shiny development by creating an account on GitHub.
126
💡 Easily improve the user experience of your Shiny apps in seconds
https://github.com/daattali/shinyjs
💡 Easily improve the user experience of your Shiny apps in seconds - daattali/shinyjs
127
Easily install and load packages from the tidyverse
https://github.com/hadley/tidyverse
Easily install and load packages from the tidyverse - tidyverse/tidyverse
128
:no_entry: ARCHIVED Accesses the Monkeylearn API for Text Classifiers and Extractors
https://github.com/masalmon/monkeylearn
:no_entry: ARCHIVED :no_entry: Accesses the Monkeylearn API for Text Classifiers and Extractors - GitHub - ropensci-archive/monkeylearn: :no_entry: ARCHIVED Accesses the Monkeylearn API for Text Cl...
129
:christmas_tree:Visualization and annotation of phylogenetic trees
https://github.com/GuangchuangYu/ggtree
:christmas_tree:Visualization and annotation of phylogenetic trees - YuLab-SMU/ggtree
130
Read SPSS, Stata and SAS files from R
https://github.com/hadley/haven
Read SPSS, Stata and SAS files from R. Contribute to tidyverse/haven development by creating an account on GitHub.
131
RPy (R from Python)
http://rpy.sourceforge.net/
Download RPy (R from Python) for free. RPy is a very simple, yet robust, Python interface to the R Programming Language. It can manage all kinds of R objects and can execute arbitrary R functions (including the graphic functions).
132
Fast and Simple MongoDB Client for R
https://github.com/jeroenooms/mongolite
Fast and Simple MongoDB Client for R. Contribute to jeroen/mongolite development by creating an account on GitHub.
133
An implementation of the Grammar of Graphics in R
https://github.com/hadley/ggplot2
An implementation of the Grammar of Graphics in R. Contribute to tidyverse/ggplot2 development by creating an account on GitHub.
134
An interactive graphing library for R
https://github.com/ropensci/plotly
An interactive graphing library for R. Contribute to plotly/plotly.R development by creating an account on GitHub.
135
Simple web scraping for R
https://github.com/hadley/rvest
Simple web scraping for R. Contribute to tidyverse/rvest development by creating an account on GitHub.
136
dplyr: A grammar of data manipulation
https://github.com/hadley/dplyr
dplyr: A grammar of data manipulation. Contribute to tidyverse/dplyr development by creating an account on GitHub.
137
A database interface (DBI) definition for communication between R and RDBMSs
https://github.com/rstats-db/DBI
A database interface (DBI) definition for communication between R and RDBMSs - r-dbi/DBI
138
🐟 A Swiss-Army Knife for Data I/O
https://github.com/leeper/rio
🐟 A Swiss-Army Knife for Data I/O. Contribute to gesistsa/rio development by creating an account on GitHub.
139
Read flat files (csv, tsv, fwf) into R
https://github.com/hadley/readr
Read flat files (csv, tsv, fwf) into R. Contribute to tidyverse/readr development by creating an account on GitHub.
140
An R package for the Quantitative Analysis of Textual Data
https://github.com/kbenoit/quanteda
An R package for the Quantitative Analysis of Textual Data - quanteda/quanteda
141
Fast reading of delimited files
https://github.com/r-lib/vroom
Fast reading of delimited files. Contribute to tidyverse/vroom development by creating an account on GitHub.
142
Posit
http://www.rstudio.org/
The best data science is open source. Posit is committed to creating incredible open-source tools for individuals, teams, and enterprises.
143
rocker-org
https://github.com/rocker-org
rocker-org has 27 repositories available. Follow their code on GitHub.
144
rOpenHealth
https://github.com/rOpenHealth
A collaborative project to build R tools facilitating access to quantitative healthcare and public health data - rOpenHealth
145
a fast interpreter and JIT for R
https://github.com/jtalbot/riposte
a fast interpreter and JIT for R. Contribute to jtalbot/riposte development by creating an account on GitHub.
146
Visualise line profiling results in R
https://github.com/hadley/lineprof
Visualise line profiling results in R. Contribute to hadley/lineprof development by creating an account on GitHub.
147
Functions for installing softwares from within R
https://github.com/talgalili/installr/
Functions for installing softwares from within R. Contribute to talgalili/installr development by creating an account on GitHub.
148
A logging package in R similar to log4j
https://github.com/zatonovo/futile.logger
A logging package in R similar to log4j. Contribute to zatonovo/futile.logger development by creating an account on GitHub.
149
Mixed-effects models in R using S4 classes and methods with RcppEigen
https://github.com/lme4/lme4
Mixed-effects models in R using S4 classes and methods with RcppEigen - lme4/lme4
150
Create Blogs and Websites with R Markdown
https://github.com/rstudio/blogdown
Create Blogs and Websites with R Markdown. Contribute to rstudio/blogdown development by creating an account on GitHub.
151
awesome-R/misc/posts.md at master · qinwf/awesome-R
https://github.com/qinwf/awesome-R/blob/master/misc/posts.md
A curated list of awesome R packages, frameworks and software. - qinwf/awesome-R
152
Glue strings to data in R. Small, fast, dependency free interpreted string literals.
https://github.com/tidyverse/glue
Glue strings to data in R. Small, fast, dependency free interpreted string literals. - tidyverse/glue
153
The Composer of ggplots
https://github.com/thomasp85/patchwork
The Composer of ggplots. Contribute to thomasp85/patchwork development by creating an account on GitHub.
154
Pry open the covers of R
https://github.com/hadley/pryr
Pry open the covers of R. Contribute to hadley/pryr development by creating an account on GitHub.
155
Drat R Archive Template
https://github.com/eddelbuettel/drat
Drat R Archive Template. Contribute to eddelbuettel/drat development by creating an account on GitHub.
156
create a map by R
https://github.com/Lchiffon/REmap
create a map by R. Contribute to Lchiffon/REmap development by creating an account on GitHub.
157
A repository of learning & R resources related to topic models
https://github.com/trinker/topicmodels_learning
A repository of learning & R resources related to topic models - GitHub - trinker/topicmodels_learning: A repository of learning & R resources related to topic models
158
English and European soccer results 1871-2022
https://github.com/jalapic/engsoccerdata
English and European soccer results 1871-2022. Contribute to jalapic/engsoccerdata development by creating an account on GitHub.
159
R package that provides complex systems datasets from the Colorado Index of Complex Networks (ICON) at https://icon.colorado.edu/.
https://github.com/rrrlw/ICON
R package that provides complex systems datasets from the Colorado Index of Complex Networks (ICON) at https://icon.colorado.edu/. - rrrlw/ICON
160
Presentation Ninja 幻灯忍者 · 写轮眼
https://github.com/yihui/xaringan
Presentation Ninja 幻灯忍者 · 写轮眼. Contribute to yihui/xaringan development by creating an account on GitHub.
161
A package for plotting maps in R with ggplot2
https://github.com/dkahle/ggmap
A package for plotting maps in R with ggplot2. Contribute to dkahle/ggmap development by creating an account on GitHub.
162
renv: Project environments for R.
https://github.com/rstudio/renv
renv: Project environments for R. Contribute to rstudio/renv development by creating an account on GitHub.
163
Write reusable, composable and modular R code
https://github.com/klmr/box
Write reusable, composable and modular R code. Contribute to klmr/box development by creating an account on GitHub.
164
rho-devel/rho
https://github.com/rho-devel/rho
Contribute to rho-devel/rho development by creating an account on GitHub.
165
Scorecard Development in R, 评分卡
https://github.com/ShichenXie/scorecard
Scorecard Development in R, 评分卡. Contribute to ShichenXie/scorecard development by creating an account on GitHub.
166
R Interface to Python
https://github.com/rstudio/reticulate
R Interface to Python. Contribute to rstudio/reticulate development by creating an account on GitHub.
167
List of courses teaching R
https://github.com/rstudio-education/rstats-ed
List of courses teaching R. Contribute to rstudio-education/rstats-ed development by creating an account on GitHub.
168
Coveralls.io - Test Coverage History and Statistics
https://coveralls.io/
The leading provider of test coverage analytics. Ensure that all your new code is fully covered, and see coverage trends emerge. Works with most CI services. Always free for open source.
169
UTF-8 Text Processing (R Package)
https://github.com/patperry/r-utf8
UTF-8 Text Processing (R Package). Contribute to patperry/r-utf8 development by creating an account on GitHub.
170
netdiffuseR: Analysis of Diffusion and Contagion Processes on Networks
https://github.com/USCCANA/netdiffuseR
netdiffuseR: Analysis of Diffusion and Contagion Processes on Networks - USCCANA/netdiffuseR
171
A guide to some of the most useful R Packages that we know about
https://github.com/rstudio/RStartHere
A guide to some of the most useful R Packages that we know about - rstudio/RStartHere
172
Efficient R programming
https://csgillespie.github.io/efficientR/
Efficient R Programming is about increasing the amount of work you can do with R in a given amount of time. It’s about both computational and programmer efficiency.
173
Welcome | R for Data Science
http://r4ds.had.co.nz/
This book will teach you how to do data science with R: You’ll learn how to get your data into R, get it into the most useful structure, transform it, visualise it and model it. In this book, you will find a practicum of skills for data science. Just as a chemist learns how to clean test tubes and stock a lab, you’ll learn how to clean data and draw plots—and many other things besides. These are the skills that allow data science to happen, and here you will find the best practices for doing each of these things with R. You’ll learn how to use the grammar of graphics, literate programming, and reproducible research to save time. You’ll also learn how to manage cognitive resources to facilitate discoveries when wrangling, visualising, and exploring data.
174
Renjin | The JVM-based interpreter for the R language for statistical computing
http://www.renjin.org/
Integrate R to Java and enhance your data analysis and statistical computing with R code and packages using Renjin, the JVM-based interpreter for the R language.
175
:lock_with_ink_pen: Opinionated, typographic-centric ggplot2 themes and theme components
https://github.com/hrbrmstr/hrbrthemes
:lock_with_ink_pen: Opinionated, typographic-centric ggplot2 themes and theme components - hrbrmstr/hrbrthemes
176
Tidy time series forecasting
https://github.com/tidyverts/fable
Tidy time series forecasting. Contribute to tidyverts/fable development by creating an account on GitHub.
177
Classes and methods for spatio-temporal data
https://github.com/edzer/spacetime
Classes and methods for spatio-temporal data. Contribute to edzer/spacetime development by creating an account on GitHub.
178
TensorFlow for R
https://github.com/rstudio/tensorflow
TensorFlow for R. Contribute to rstudio/tensorflow development by creating an account on GitHub.
179
R package, using vis.js library for network visualization
https://github.com/datastorm-open/visNetwork
R package, using vis.js library for network visualization - datastorm-open/visNetwork
180
Download and use Census TIGER/Line shapefiles in R
https://github.com/walkerke/tigris
Download and use Census TIGER/Line shapefiles in R - walkerke/tigris
181
A drat repository for R Package releases including the R COBOL Data Integration (rcoboldi) and R Bitcoincharts.com API packages (rbitcoinchartsapi).
https://github.com/thospfuller/drat
A drat repository for R Package releases including the R COBOL Data Integration (rcoboldi) and R Bitcoincharts.com API packages (rbitcoinchartsapi). - thospfuller/drat
182
Codecov - The Leading Code Coverage Solution
https://codecov.io/.
Code coverage reporting solution for any test suite — Codecov gives developers actionable insights to deploy reliable code with confidence.
183
Umbrella package of the 'spatstat' family................
https://github.com/spatstat/spatstat
Umbrella package of the 'spatstat' family................ - GitHub - spatstat/spatstat: Umbrella package of the 'spatstat' family................
184
A functional programming toolkit for R
https://github.com/tidyverse/purrr
A functional programming toolkit for R. Contribute to tidyverse/purrr development by creating an account on GitHub.
185
A log4j derivative for R.
https://github.com/johnmyleswhite/log4r
A log4j derivative for R. Contribute to johnmyleswhite/log4r development by creating an account on GitHub.
186
R-bloggers
http://www.r-bloggers.com/
R news and tutorials contributed by hundreds of R bloggers
187
Easily install and load packages from the tidyverse
https://github.com/tidyverse/tidyverse
Easily install and load packages from the tidyverse - tidyverse/tidyverse
188
A tidy API for graph manipulation
https://github.com/thomasp85/tidygraph
A tidy API for graph manipulation. Contribute to thomasp85/tidygraph development by creating an account on GitHub.
189
Accelerated Container Application Development
https://www.docker.com/.
Docker is a platform designed to help developers build, share, and run container applications. We handle the tedious setup, so you can focus on the code.
190
Exploratory Data Analysis with R
https://leanpub.com/exdata
This book teaches you to use R to visualize and explore data, a key element of the data science process.
191
Report Writing for Data Science in R
https://leanpub.com/reportwriting
This book teaches the concepts and tools behind reporting modern data analyses in a reproducible manner.
192
R package for thematic maps
https://github.com/mtennekes/tmap
R package for thematic maps. Contribute to mtennekes/tmap development by creating an account on GitHub.
193
A curated list of awesome network analysis resources.
https://github.com/briatte/awesome-network-analysis
A curated list of awesome network analysis resources. - briatte/awesome-network-analysis
194
R bindings to the libgit2 library
https://github.com/ropensci/git2r
R bindings to the libgit2 library. Contribute to ropensci/git2r development by creating an account on GitHub.
195
Readings in applied data science
https://github.com/hadley/stats337
Readings in applied data science. Contribute to hadley/stats337 development by creating an account on GitHub.
196
R COBOL DI (Data Integration) Package : Import COBOL CopyBook data files directly into R as properly structured data frames.
https://github.com/thospfuller/rcoboldi
R COBOL DI (Data Integration) Package : Import COBOL CopyBook data files directly into R as properly structured data frames. - thospfuller/rcoboldi
197
a curated list of R tutorials for Data Science, NLP and Machine Learning
https://github.com/ujjwalkarn/DataScienceR
a curated list of R tutorials for Data Science, NLP and Machine Learning - GitHub - ujjwalkarn/DataScienceR: a curated list of R tutorials for Data Science, NLP and Machine Learning
198
📜 Discover and install useful RStudio addins
https://github.com/daattali/addinslist
📜 Discover and install useful RStudio addins . Contribute to daattali/addinslist development by creating an account on GitHub.
199
R in Action, Second Edition
http://www.manning.com/kabacoff2/
R in Action, Second Edition</i> presents both the R language and the examples that make it so useful for business developers. Focusing on practical solutions, the book offers a crash course in statistics and covers elegant methods for dealing with messy and incomplete data that are difficult to analyze using traditional methods. You'll also master R's extensive graphical capabilities for exploring and presenting data visually. And this expanded second edition includes new chapters on time series analysis, cluster analysis, and classification methodologies, including decision trees, random forests, and support vector machines.</p>
200
R Cookbook, 2nd Edition
http://shop.oreilly.com/product/0636920174851.do
Perform data analysis with R quickly and efficiently with more than 275 practical recipes in this expanded second edition. The R language provides everything you need to do statistical work, … - Selection from R Cookbook, 2nd Edition [Book]
201
The Art of R Programming
http://shop.oreilly.com/product/9781593273842.do
R is the world's most popular language for developing statistical software: Archaeologists use it to track the spread of ancient civilizations, drug companies use it to discover which medications are … - Selection from The Art of R Programming [Book]
202
R Programming for Data Science
https://leanpub.com/rprogramming
Learn the fundamentals for R programming and gain the tools needed for doing data science.
203
A curated list of #rstats books
https://github.com/RomanTsegelskyi/rbooks
A curated list of #rstats books. Contribute to RomanTsegelskyi/rbooks development by creating an account on GitHub.
204
Code Courses | Pluralsight
http://tryr.codeschool.com/
We've integrated the interactivity from Code School into the Pluralsight platform. Grow your skills with code courses, assessments, paths and expert-led content on today’s most in-demand technologies.
205
Static Code Analysis for R
https://github.com/jimhester/lintr
Static Code Analysis for R. Contribute to r-lib/lintr development by creating an account on GitHub.
206
Generate R package documentation from inline R comments
https://github.com/klutometis/roxygen
Generate R package documentation from inline R comments - r-lib/roxygen2
207
An R 📦 to make testing 😀
https://github.com/hadley/testthat
An R 📦 to make testing 😀. Contribute to r-lib/testthat development by creating an account on GitHub.
208
Test coverage reports for R
https://github.com/jimhester/covr
Test coverage reports for R. Contribute to r-lib/covr development by creating an account on GitHub.
209
An Import Mechanism For R
https://github.com/smbache/import/
An Import Mechanism For R. Contribute to rticulate/import development by creating an account on GitHub.
210
Solving complex, industry-specific problems at the speed of thought
http://spotfire.tibco.com/discover-spotfire/what-does-spotfire-do/predictive-analytics/tibco-enterprise-runtime-for-r-terr
Spotfire is a visual data science platform that makes smart people smarter by combining interactive visualizations and advanced analytics to solve complex industry specific business problems.
211
:no_entry: ARCHIVED
https://github.com/ropensci/opendata
:no_entry: ARCHIVED :no_entry: . Contribute to ropensci-archive/opendata development by creating an account on GitHub.
212
Build software better, together
https://github.com/BZRLC/R-notes/blob/master/NLP/readme.md
GitHub is where people build software. More than 100 million people use GitHub to discover, fork, and contribute to over 420 million projects.
213
Generate roxygen2 skeletons populated with information scraped from the function script.
https://github.com/metrumresearchgroup/sinew
Generate roxygen2 skeletons populated with information scraped from the function script. - yonicd/sinew
214
Home
https://rweekly.org
Learn R, R tutorials, R resources, blog posts and the latest updates about the statistical programming R language.
215
CRAN Task View: WebTechnologies
https://github.com/ropensci/webservices
CRAN Task View: WebTechnologies. Contribute to cran-task-views/WebTechnologies development by creating an account on GitHub.
216
Spatial and spatio-temporal geostatistical modelling, prediction and simulation
https://github.com/edzer/gstat
Spatial and spatio-temporal geostatistical modelling, prediction and simulation - r-spatial/gstat
217
Tool for producing high quality forecasts for time series data that has multiple seasonality with linear or non-linear growth.
https://github.com/facebookincubator/prophet
Tool for producing high quality forecasts for time series data that has multiple seasonality with linear or non-linear growth. - facebook/prophet
218
:no_entry: ARCHIVED
https://github.com/ropensci/PackageDevelopment
:no_entry: ARCHIVED :no_entry: . Contribute to ropensci-archive/PackageDevelopment development by creating an account on GitHub.
219
Encapsulated object-oriented programming for R
https://github.com/wch/R6
Encapsulated object-oriented programming for R. Contribute to r-lib/R6 development by creating an account on GitHub.
220
Excerpt from the Gapminder data, as an R data package and in plain text delimited form
http://github.com/jennybc/gapminder
Excerpt from the Gapminder data, as an R data package and in plain text delimited form - jennybc/gapminder
221
Render bits of R code for sharing, e.g., on GitHub or StackOverflow.
https://github.com/jennybc/reprex
Render bits of R code for sharing, e.g., on GitHub or StackOverflow. - tidyverse/reprex
222
Tools to make an R developer's life easier
https://github.com/hadley/devtools
Tools to make an R developer's life easier. Contribute to r-lib/devtools development by creating an account on GitHub.
223
Generate static html documentation for an R package
https://github.com/hadley/staticdocs
Generate static html documentation for an R package - r-lib/pkgdown
224
📜 Discover and install useful RStudio addins
https://github.com/daattali/rstudio-addins
📜 Discover and install useful RStudio addins . Contribute to daattali/addinslist development by creating an account on GitHub.
225
Data Science
https://www.coursera.org/specialization/jhudatascience/1
Offered by Johns Hopkins University. Launch Your Career in Data Science. A ten-course introduction to data science, developed and taught by ... Enroll for free.
226
Use R! | Book titles in this series
http://www.springer.com/series/6991?detailsPage=titles
This series of inexpensive and focused books on R is aimed at practitioners. Books can discuss the use of R in a particular subject area (e.g., epidemiology, ...

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