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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
ggtreeversion can be found on https://github.com/GuangchuangYu/plotTree-ggtree.
- A
- 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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## 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
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## 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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