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Two methods for mapping and visualizing associated data on phylogeny using ggtree

If you use this work in published research, please cite:

G Yu<sup>*</sup>, TTY Lam, H Zhu, Y Guan<sup>*</sup>. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(12):3041-3043, https://doi.org/10.1093/molbev/msy194.


This repo contains source code to produce Supplementary Material of the above paper.

To compile the supplemental_file.pdf, please run the following command in R:

rmarkdown::render('supplemental_file.Rmd')

Here is the output of devtools::session_info() on the system on which the document was compiled:

## Session info -------------------------------------------------------------

##  setting  value                       
##  version  R version 3.5.0 (2018-04-23)
##  system   x86_64, linux-gnu           
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  tz       Asia/Hong_Kong              
##  date     2018-07-23

## Packages -----------------------------------------------------------------

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##  ape           * 5.1       2018-04-04 CRAN (R 3.5.0)
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##  backports       1.1.2     2017-12-13 CRAN (R 3.5.0)
##  base          * 3.5.0     2018-05-24 local         
##  bindr           0.1.1     2018-03-13 CRAN (R 3.5.0)
##  bindrcpp      * 0.2.2     2018-03-29 CRAN (R 3.5.0)
##  Biobase         2.40.0    2018-07-18 Bioconductor  
##  BiocGenerics  * 0.26.0    2018-07-18 Bioconductor  
##  biomformat      1.8.0     2018-07-22 Bioconductor  
##  Biostrings    * 2.48.0    2018-07-22 Bioconductor  
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##  commonmark      1.5       2018-04-28 CRAN (R 3.5.0)
##  compiler        3.5.0     2018-05-24 local         
##  cowplot         0.9.3     2018-07-15 CRAN (R 3.5.0)
##  crayon          1.3.4     2017-09-16 CRAN (R 3.5.0)
##  curl            3.2       2018-03-28 CRAN (R 3.5.0)
##  data.table      1.11.4    2018-05-27 CRAN (R 3.5.0)
##  datasets      * 3.5.0     2018-05-24 local         
##  devtools        1.13.6    2018-06-27 CRAN (R 3.5.0)
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##  ggstance        0.3       2016-11-16 CRAN (R 3.5.0)
##  ggtree        * 1.12.5    2018-07-19 Bioconductor  
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##  graphics      * 3.5.0     2018-05-24 local         
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##  grid            3.5.0     2018-05-24 local         
##  gridGraphics    0.3-0     2018-04-03 CRAN (R 3.5.0)
##  gtable          0.2.0     2016-02-26 CRAN (R 3.5.0)
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##  jsonlite        1.5       2017-06-01 CRAN (R 3.5.0)
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##  knitr           1.20      2018-02-20 CRAN (R 3.5.0)
##  labeling        0.3       2014-08-23 CRAN (R 3.5.0)
##  lattice         0.20-35   2017-03-25 CRAN (R 3.5.0)
##  lazyeval        0.2.1     2017-10-29 CRAN (R 3.5.0)
##  magick          1.9       2018-05-11 CRAN (R 3.5.0)
##  magrittr      * 1.5       2014-11-22 CRAN (R 3.5.0)
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##  parallel      * 3.5.0     2018-05-24 local         
##  permute         0.9-4     2016-09-09 CRAN (R 3.5.0)
##  phylobase     * 0.8.4     2017-04-21 CRAN (R 3.5.0)
##  phyloseq      * 1.24.2    2018-07-15 Bioconductor  
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##  plyr            1.8.4     2016-06-08 CRAN (R 3.5.0)
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##  progress        1.2.0     2018-06-14 CRAN (R 3.5.0)
##  purrr           0.2.5     2018-05-29 CRAN (R 3.5.0)
##  R6              2.2.2     2017-06-17 CRAN (R 3.5.0)
##  RColorBrewer    1.1-2     2014-12-07 CRAN (R 3.5.0)
##  Rcpp            0.12.17   2018-05-18 CRAN (R 3.5.0)
##  readr           1.1.1     2017-05-16 CRAN (R 3.5.0)
##  reshape2        1.4.3     2017-12-11 CRAN (R 3.5.0)
##  RevoUtils     * 11.0.0    2018-06-04 local         
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##  rhdf5           2.24.0    2018-07-22 Bioconductor  
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##  rmarkdown     * 1.10      2018-06-11 CRAN (R 3.5.0)
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##  stats         * 3.5.0     2018-05-24 local         
##  stats4        * 3.5.0     2018-05-24 local         
##  stringi         1.2.4     2018-07-20 CRAN (R 3.5.0)
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##  tidytree        0.1.9     2018-06-13 CRAN (R 3.5.0)
##  tinytex         0.6       2018-07-07 CRAN (R 3.5.0)
##  tools           3.5.0     2018-05-24 local         
##  treeio        * 1.4.2     2018-07-19 Bioconductor  
##  utils         * 3.5.0     2018-05-24 local         
##  uuid            0.1-2     2015-07-28 CRAN (R 3.5.0)
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