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
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 -----------------------------------------------------------------
## package * version date source
## ade4 1.7-11 2018-04-05 CRAN (R 3.5.0)
## ape * 5.1 2018-04-04 CRAN (R 3.5.0)
## assertthat 0.2.0 2017-04-11 CRAN (R 3.5.0)
## 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)
## methods * 3.5.0 2018-05-24 local
## mgcv 1.8-24 2018-06-18 CRAN (R 3.5.0)
## multtest 2.36.0 2018-07-22 Bioconductor
## munsell 0.5.0 2018-06-12 CRAN (R 3.5.0)
## 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)
## rncl 0.8.2 2016-12-16 CRAN (R 3.5.0)
## RNeXML 2.1.1 2018-05-07 CRAN (R 3.5.0)
## roxygen2 * 6.0.1 2017-02-06 CRAN (R 3.5.0)
## rprojroot 1.3-2 2018-01-03 CRAN (R 3.5.0)
## rstudioapi 0.7 2017-09-07 CRAN (R 3.5.0)
## rvcheck * 0.1.0 2018-05-23 CRAN (R 3.5.0)
## rvest 0.3.2 2016-06-17 CRAN (R 3.5.0)
## S4Vectors * 0.18.3 2018-07-18 Bioconductor
## scales 0.5.0 2017-08-24 CRAN (R 3.5.0)
## splines 3.5.0 2018-05-24 local
## 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)
## stringr 1.3.1 2018-05-10 CRAN (R 3.5.0)
## survival 2.42-6 2018-07-13 CRAN (R 3.5.0)
## tibble * 1.4.2 2018-01-22 CRAN (R 3.5.0)
## tidyr * 0.8.1 2018-05-18 CRAN (R 3.5.0)
## tidyselect 0.2.4 2018-02-26 CRAN (R 3.5.0)
## 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)
## vegan 2.5-2 2018-05-17 CRAN (R 3.5.0)
## viridisLite 0.3.0 2018-02-01 CRAN (R 3.5.0)
## withr 2.1.2 2018-03-15 CRAN (R 3.5.0)
## 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