If you use this work in published research, please cite:
S Xu, Z Dai, P Guo, X Fu, S Liu, L Zhou, W Tang, T Feng, M Chen, L Zhan, T Wu, E Hu, Y Jiang*, X Bo* and G Yu*. ggtreeExtra: Compact visualization of richly annotated phylogenetic data. Molecular Biology and Evolution. 2021, msab166. doi: 10.1093/molbev/msab166 (accepted).
This repo contains source code and data to produce
Supplementary Material of the above paper.- rawdata: contains
HMP_tree,keggandPhyloPhlAn, downloaded from the examples of GraPhlAn, and theMethanotroph, downloaded from the repo. - scripts: contains the script to produce the dataset of
datausing the data set ofrawdata. - data: contains all the data sets that used to generate figures in Supplemental file.
- Rmarkdown: contains the source code to produce Supplementary File.
- R (>= 4.0.3) should be installed and located in the user’s PATH,
and the following packages should be installed.
ggtreeExtra:BiocManager::install("ggtreeExtra")ggtree:BiocManager::install("ggtree")treeio:BiocManager::install("treeio")tidytree:install.packages("tidytree")ggplot2:install.packages("ggplot2")kableExtra:install.packages("kableExtra")bookdown:install.package("bookdown")MicrobiotaProcess:BiocManager::install("MicrobiotaProcess")ggstar:install.packages("ggstar")Cairo:install.packages("Cairo")aplot:install.packages("aplot")patchwork:install.packages("patchwork")ggnewscale:install.packages("ggnewscale")knitr:install.packages("knitr")ggpmisc:install.packages("ggpmisc")ggpattern:remotes::install_github("coolbutuseless/ggpattern")tibble:install.packages("tibble")tidyr:install.packages("tidyr")dplyr:install.packages("dplyr")ggimage:install.packages("ggimage")ggridges:install.packages("ggridges")
To compile the Rmarkdown/supplemental_file.pdf, please run the following command on terminal.
Rscript -e 'rmarkdown::render("./Rmarkdown/supplementary_file.Rmd")'Or run the following command in R.
rmarkdown::render("./Rmarkdown/supplementary_file.Rmd")Here is the output of sessionInfo() of the system on which the
Supplemental file was compiled:
## R version 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.4 LTS
##
## Matrix products: default
## BLAS: /mnt/d/UbuntuApps/R/4.0.3/lib/R/lib/libRblas.so
## LAPACK: /mnt/d/UbuntuApps/R/4.0.3/lib/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] ggimage_0.2.8 tibble_3.1.0 dplyr_1.0.5
## [4] tidyr_1.1.2 ggridges_0.5.2 ggpmisc_0.3.7
## [7] ggpattern_0.1.3 knitr_1.30 patchwork_1.0.1
## [10] Cairo_1.5-12.2 kableExtra_1.3.1 aplot_0.0.6
## [13] MicrobiotaProcess_1.2.1 ggnewscale_0.4.3 tidytree_0.3.4
## [16] treeio_1.14.4 ggtree_2.4.2 ggplot2_3.3.2
## [19] ggstar_1.0.2 ggtreeExtra_1.0.4
##
## loaded via a namespace (and not attached):
## [1] TH.data_1.0-10 colorspace_1.4-1 ggsignif_0.6.0
## [4] class_7.3-17 ellipsis_0.3.1 modeltools_0.2-23
## [7] XVector_0.30.0 rstudioapi_0.11 ggrepel_0.8.2
## [10] fansi_0.4.2 mvtnorm_1.1-1 coin_1.3-1
## [13] xml2_1.3.2 codetools_0.2-16 splines_4.0.3
## [16] libcoin_1.0-6 polyclip_1.10-0 ade4_1.7-16
## [19] jsonlite_1.7.2 phyloseq_1.34.0 cluster_2.1.0
## [22] png_0.1-7 BiocManager_1.30.10 compiler_4.0.3
## [25] httr_1.4.2 rvcheck_0.1.8 assertthat_0.2.1
## [28] Matrix_1.2-18 lazyeval_0.2.2 htmltools_0.5.0
## [31] prettyunits_1.1.1 tools_4.0.3 igraph_1.2.6
## [34] gtable_0.3.0 glue_1.4.2 reshape2_1.4.4
## [37] Rcpp_1.0.6 Biobase_2.50.0 vctrs_0.3.6
## [40] Biostrings_2.58.0 rhdf5filters_1.2.0 multtest_2.46.0
## [43] ape_5.4-1 nlme_3.1-150 iterators_1.0.13
## [46] xfun_0.19 stringr_1.4.0 Rmisc_1.5
## [49] rvest_0.3.6 lifecycle_1.0.0 gtools_3.8.2
## [52] zlibbioc_1.36.0 MASS_7.3-53 zoo_1.8-8
## [55] scales_1.1.1 hms_0.5.3 parallel_4.0.3
## [58] biomformat_1.18.0 sandwich_3.0-0 rhdf5_2.34.0
## [61] yaml_2.2.1 gridGeometry_0.2-0 gridExtra_2.3
## [64] reshape_0.8.8 stringi_1.5.3 S4Vectors_0.28.0
## [67] foreach_1.5.1 e1071_1.7-4 permute_0.9-5
## [70] BiocGenerics_0.36.0 rlang_0.4.10 pkgconfig_2.0.3
## [73] matrixStats_0.57.0 evaluate_0.14 lattice_0.20-41
## [76] sf_0.9-6 purrr_0.3.4 Rhdf5lib_1.12.0
## [79] tidyselect_1.1.0 plyr_1.8.6 magrittr_2.0.1
## [82] R6_2.5.0 IRanges_2.24.0 magick_2.5.2
## [85] generics_0.1.0 multcomp_1.4-14 DBI_1.1.0
## [88] pillar_1.5.1 withr_2.3.0 mgcv_1.8-33
## [91] units_0.6-7 survival_3.2-7 crayon_1.4.1
## [94] KernSmooth_2.23-18 utf8_1.2.1 rmarkdown_2.5
## [97] progress_1.2.2 grid_4.0.3 data.table_1.13.2
## [100] vegan_2.5-6 classInt_0.4-3 digest_0.6.27
## [103] webshot_0.5.2 gridGraphics_0.5-0 stats4_4.0.3
## [106] munsell_0.5.0 ggplotify_0.0.5 viridisLite_0.3.0
We also provided a docker image to help users to build the computing environment. You can pull and run it according to the following commands.
- Install Docker (https://www.docker.com/)
sudo apt-get install docker.io(Ubuntu)
- Pull the Docker image from Docker Hub:
docker pull xushuangbin/ggtreeextraarticleenv:latest- or
sudo pull xushuangbin/ggtreeextraarticleenv:latest
- Run the image:
docker run -e PASSWORD=yourpassword -p 8787:8787 xushuangbin/ggtreeextraarticleenv- or
sudo docker run -e PASSWORD=yourpassword -p 8787:8787 xushuangbin/ggtreeextraarticleenv
- Log in to RStudio at http://localhost:8787 using username
rstudioand passwordyourpassword. For Windows users, you also need to provide your IP address, you can find it usingdocker-machine ip default. - Inside the RStudio, run:
browseVignettes(package = "ggtreeExtraArticleEnv") - You can click one of the links: “PDF”, “source”, “R code”
- In case of
The requested page was not founderror, try add ‘help/’ in front of the hostname in the URL (this is a known bug): http://localhost:8787/help/library/ggtreeExtraArticleEnv/doc/supplementary_file.pdf