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, 38(9):4039-4042. doi: 10.1093/molbev/msab166.
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")ggpp:install.packages("ggpp")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 4.1.0 (2021-05-18)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.4 LTS
##
## Matrix products: default
## BLAS: /mnt/d/UbuntuApps/R/4.1.0/lib/R/lib/libRblas.so
## LAPACK: /mnt/d/UbuntuApps/R/4.1.0/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_0.2.9 tibble_3.1.2
## [3] dplyr_1.0.7 tidyr_1.1.3
## [5] ggridges_0.5.3 ggpp_0.4.0
## [7] ggpattern_0.1.3 knitr_1.33
## [9] patchwork_1.1.1 Cairo_1.5-12.2
## [11] kableExtra_1.3.4 aplot_0.0.6
## [13] MicrobiotaProcess_1.5.3.992 ggnewscale_0.4.5
## [15] tidytree_0.3.4.991 treeio_1.17.2
## [17] ggtree_3.1.3.991 ggplot2_3.3.5
## [19] ggstar_1.0.2.991 ggtreeExtra_1.3.3
##
## loaded via a namespace (and not attached):
## [1] TH.data_1.0-10 colorspace_2.0-2
## [3] ggsignif_0.6.3 class_7.3-19
## [5] ellipsis_0.3.2 modeltools_0.2-23
## [7] XVector_0.32.0 GenomicRanges_1.44.0
## [9] proxy_0.4-26 rstudioapi_0.13
## [11] ggrepel_0.9.1 fansi_0.5.0
## [13] mvtnorm_1.1-2 coin_1.4-1
## [15] xml2_1.3.2 codetools_0.2-18
## [17] splines_4.1.0 libcoin_1.0-8
## [19] polyclip_1.10-0 ade4_1.7-17
## [21] jsonlite_1.7.2 phyloseq_1.36.0
## [23] cluster_2.1.2 png_0.1-7
## [25] compiler_4.1.0 httr_1.4.2
## [27] assertthat_0.2.1 Matrix_1.3-4
## [29] lazyeval_0.2.2 htmltools_0.5.1.1
## [31] tools_4.1.0 igraph_1.2.6
## [33] gtable_0.3.0 glue_1.4.2
## [35] GenomeInfoDbData_1.2.6 reshape2_1.4.4
## [37] Rcpp_1.0.6 Biobase_2.52.0
## [39] vctrs_0.3.8 Biostrings_2.60.1
## [41] rhdf5filters_1.4.0 multtest_2.48.0
## [43] ape_5.5 svglite_2.0.0
## [45] nlme_3.1-152 iterators_1.0.13
## [47] xfun_0.24 stringr_1.4.0
## [49] rvest_1.0.0 lifecycle_1.0.0
## [51] zlibbioc_1.38.0 MASS_7.3-54
## [53] zoo_1.8-9 scales_1.1.1
## [55] MatrixGenerics_1.4.0 parallel_4.1.0
## [57] SummarizedExperiment_1.22.0 biomformat_1.20.0
## [59] sandwich_3.0-1 rhdf5_2.36.0
## [61] yaml_2.2.1 gridGeometry_0.2-0
## [63] gridExtra_2.3 ggfun_0.0.3
## [65] yulab.utils_0.0.3 stringi_1.6.2
## [67] S4Vectors_0.30.0 foreach_1.5.1
## [69] e1071_1.7-7 permute_0.9-5
## [71] BiocGenerics_0.38.0 GenomeInfoDb_1.28.0
## [73] rlang_0.4.11 pkgconfig_2.0.3
## [75] systemfonts_1.0.2 matrixStats_0.59.0
## [77] bitops_1.0-7 evaluate_0.14
## [79] lattice_0.20-44 sf_1.0-0
## [81] purrr_0.3.4 Rhdf5lib_1.14.1
## [83] tidyselect_1.1.1 plyr_1.8.6
## [85] magrittr_2.0.1 R6_2.5.0
## [87] IRanges_2.26.0 magick_2.7.2
## [89] generics_0.1.0 multcomp_1.4-17
## [91] DelayedArray_0.18.0 DBI_1.1.1
## [93] pillar_1.6.1 withr_2.4.2
## [95] mgcv_1.8-36 units_0.7-2
## [97] survival_3.2-11 RCurl_1.98-1.3
## [99] crayon_1.4.1 KernSmooth_2.23-20
## [101] utf8_1.2.1 rmarkdown_2.9.7
## [103] grid_4.1.0 data.table_1.14.0
## [105] vegan_2.5-7 classInt_0.4-3
## [107] digest_0.6.27 webshot_0.5.2
## [109] gridGraphics_0.5-1 stats4_4.1.0
## [111] munsell_0.5.0 ggplotify_0.0.9
## [113] viridisLite_0.4.0
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