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plotting_tree_with_data

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

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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.

+ plotTree: downloaded from <https://github.com/katholt/plotTree>, access date: 2018-07-23
    - A `ggtree` version can be found on <https://github.com/GuangchuangYu/plotTree-ggtree>.
+ HPV58.tree: newick text of the HPV58 tree published on <http://jvi.asm.org/content/91/21/e01285-17>.
+ HPV58_aln.fas: aligned tip sequences of `HPV58.tree`
+ header.tex: LaTeX packages that used to compile the PDF
+ supp.bib: bibliography
+ supplmental_file.Rmd: R Markdown file to compile the PDF
+ supplemental_file.pdf: Supplemental Material, the PDF

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

```r
rmarkdown::render('supplemental_file.Rmd')
```

Here is the output of `devtools::session_info()` on the system on which [the document](https://github.com/GuangchuangYu/plotting_tree_with_data/blob/master/supplemental_file.pdf) 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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    ##  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  
    ##  Cairo           1.5-9     2015-09-26 CRAN (R 3.5.0)
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    ##  data.table      1.11.4    2018-05-27 CRAN (R 3.5.0)
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    ##  ggtree        * 1.12.5    2018-07-19 Bioconductor  
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    ##  graphics      * 3.5.0     2018-05-24 local         
    ##  grDevices     * 3.5.0     2018-05-24 local         
    ##  grid            3.5.0     2018-05-24 local         
    ##  gridGraphics    0.3-0     2018-04-03 CRAN (R 3.5.0)
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    ##  IRanges       * 2.14.10   2018-07-18 Bioconductor  
    ##  iterators       1.0.10    2018-06-01 local         
    ##  jsonlite        1.5       2017-06-01 CRAN (R 3.5.0)
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    ##  magrittr      * 1.5       2014-11-22 CRAN (R 3.5.0)
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    ##  purrr           0.2.5     2018-05-29 CRAN (R 3.5.0)
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    ##  zlibbioc        1.26.0    2018-07-22 Bioconductor

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