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Showing content from https://github.com/GuangchuangYu/plotting_tree_with_data below:

GuangchuangYu/plotting_tree_with_data: Two methods for mapping and visualizing associated data on phylogeny using ggtree

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

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

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(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:

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  
##  Cairo           1.5-9     2015-09-26 CRAN (R 3.5.0)
##  cluster         2.0.7-1   2018-04-13 CRAN (R 3.5.0)
##  codetools       0.2-15    2016-10-05 CRAN (R 3.5.0)
##  colorspace      1.3-2     2016-12-14 CRAN (R 3.5.0)
##  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)
##  digest          0.6.15    2018-01-28 CRAN (R 3.5.0)
##  dplyr         * 0.7.6     2018-06-29 CRAN (R 3.5.0)
##  evaluate        0.11      2018-07-17 CRAN (R 3.5.0)
##  foreach         1.5.0     2018-06-01 local         
##  ggimage       * 0.1.7     2018-06-19 CRAN (R 3.5.0)
##  ggplot2       * 3.0.0     2018-07-03 CRAN (R 3.5.0)
##  ggplotify       0.0.2     2018-04-24 CRAN (R 3.5.0)
##  ggridges      * 0.5.0     2018-04-05 CRAN (R 3.5.0)
##  ggstance        0.3       2016-11-16 CRAN (R 3.5.0)
##  ggtree        * 1.12.5    2018-07-19 Bioconductor  
##  glue            1.3.0     2018-07-17 CRAN (R 3.5.0)
##  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)
##  gtable          0.2.0     2016-02-26 CRAN (R 3.5.0)
##  hms             0.4.2     2018-03-10 CRAN (R 3.5.0)
##  htmltools       0.3.6     2017-04-28 CRAN (R 3.5.0)
##  httr            1.3.1     2017-08-20 CRAN (R 3.5.0)
##  igraph          1.2.1     2018-03-10 CRAN (R 3.5.0)
##  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)
##  kableExtra    * 0.9.0     2018-05-21 CRAN (R 3.5.0)
##  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)
##  MASS            7.3-50    2018-04-30 CRAN (R 3.5.0)
##  Matrix          1.2-14    2018-04-13 CRAN (R 3.5.0)
##  memoise         1.1.0     2017-04-21 CRAN (R 3.5.0)
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##  mgcv            1.8-24    2018-06-18 CRAN (R 3.5.0)
##  multtest        2.36.0    2018-07-22 Bioconductor  
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##  nlme            3.1-137   2018-04-07 CRAN (R 3.5.0)
##  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  
##  pillar          1.3.0     2018-07-14 CRAN (R 3.5.0)
##  pkgconfig       2.0.1     2017-03-21 CRAN (R 3.5.0)
##  plyr            1.8.4     2016-06-08 CRAN (R 3.5.0)
##  prettyunits     1.0.2     2015-07-13 CRAN (R 3.5.0)
##  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         
##  RevoUtilsMath * 11.0.0    2018-06-01 local         
##  rhdf5           2.24.0    2018-07-22 Bioconductor  
##  Rhdf5lib        1.2.1     2018-07-22 Bioconductor  
##  rlang           0.2.1     2018-05-30 CRAN (R 3.5.0)
##  rmarkdown     * 1.10      2018-06-11 CRAN (R 3.5.0)
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##  RNeXML          2.1.1     2018-05-07 CRAN (R 3.5.0)
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##  splines         3.5.0     2018-05-24 local         
##  stats         * 3.5.0     2018-05-24 local         
##  stats4        * 3.5.0     2018-05-24 local         
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##  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)
##  vegan           2.5-2     2018-05-17 CRAN (R 3.5.0)
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##  xfun            0.3       2018-07-06 CRAN (R 3.5.0)
##  XML             3.98-1.12 2018-07-15 CRAN (R 3.5.0)
##  xml2            1.2.0     2018-01-24 CRAN (R 3.5.0)
##  XVector       * 0.20.0    2018-07-22 Bioconductor  
##  yaml            2.1.19    2018-05-01 CRAN (R 3.5.0)
##  zlibbioc        1.26.0    2018-07-22 Bioconductor

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