If you use this work in published research, please cite:
S Xu#, M Chen#, T Feng, L Zhan, L Zhou, G Yu*. Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers. Frontiers in Genetics. 2021, 12:774846. doi: 10.3389/fgene.2021.774846
This repo contains source code and data to produce Supplementary Material of the above paper.
- supplementary.Rmd: R Markdown file to compile the PDF
- supplementary.pdf: Supplemental Material, the PDF
- header.tex: LaTeX packages that used to compile the PDF
- 7MWE_A.csv: the amino acid hydrophobicity or hydrophilicity scales output of human E3 ubiquitin-protein ligase HUWE1 Chain A(NCBI_id:7MWE_A) using Expasy-Protscale with default parameters.
- gp200.nwk: newick text of gp200 tree was published on https://europepmc.org/article/MED/21113103.
- GCST90007012_buildGRCh37.tsv : SNP data was collected from GWAS Catalog and published on https://www.nature.com/articles/s42003-020-01416-z.
- data1.txt: microbe relative abundance data was published on https://www.sciencedirect.com/science/article/abs/pii/S0048969719352659.
- sigdata.rda: significant levels of microbe relative abundance data was published on https://www.sciencedirect.com/science/article/abs/pii/S0048969719352659.
To compile the supplemental_file.pdf, please run the following command in R:
rmarkdown::render('supplementary.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 4.1.1 (2021-08-10)
# os Windows 10 x64
# system x86_64, mingw32
# ui RStudio
# language (EN)
# collate Chinese (Simplified)_China.936
# ctype Chinese (Simplified)_China.936
# tz Asia/Taipei
# date 2021-09-07
#
# - Packages ----------------------------------------------------------------------------------------------------
# package * version date lib source
# ape 5.5 2021-04-25 [1] CRAN (R 4.1.1)
# aplot 0.0.7 2021-09-01 [1] CRAN (R 4.1.1)
# bookdown 0.24 2021-09-02 [1] CRAN (R 4.1.1)
# cachem 1.0.6 2021-08-19 [1] CRAN (R 4.1.1)
# callr 3.7.0 2021-04-20 [1] CRAN (R 4.1.1)
# cli 3.0.1 2021-07-17 [1] CRAN (R 4.1.0)
# colorspace 2.0-2 2021-06-24 [1] CRAN (R 4.1.1)
# cowplot 1.1.1 2020-12-30 [1] CRAN (R 4.1.1)
# crayon 1.4.1 2021-02-08 [1] CRAN (R 4.1.1)
# desc 1.3.0 2021-03-05 [1] CRAN (R 4.1.1)
# devtools 2.4.2 2021-06-07 [1] CRAN (R 4.1.1)
# digest 0.6.27 2020-10-24 [1] CRAN (R 4.1.1)
# dplyr 1.0.7 2021-06-18 [1] CRAN (R 4.1.0)
# ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.1.0)
# evaluate 0.14 2019-05-28 [1] CRAN (R 4.1.1)
# fansi 0.5.0 2021-05-25 [1] CRAN (R 4.1.1)
# farver 2.1.0 2021-02-28 [1] CRAN (R 4.1.1)
# fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.1.1)
# fs 1.5.0 2020-07-31 [1] CRAN (R 4.1.1)
# generics 0.1.0 2020-10-31 [1] CRAN (R 4.1.1)
# ggbreak * 0.0.4 2021-08-14 [1] CRAN (R 4.1.1)
# ggfun 0.0.3 2021-08-17 [1] CRAN (R 4.1.1)
# ggplot2 * 3.3.5 2021-06-25 [1] CRAN (R 4.1.0)
# ggplotify 0.1.0 2021-09-02 [1] CRAN (R 4.1.1)
# ggtree * 3.0.4 2021-08-22 [1] Bioconductor
# glue 1.4.2 2020-08-27 [1] CRAN (R 4.1.1)
# gridGraphics 0.5-1 2020-12-13 [1] CRAN (R 4.1.1)
# gtable 0.3.0 2019-03-25 [1] CRAN (R 4.1.1)
# htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.1.1)
# jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.1.1)
# knitr 1.33 2021-04-24 [1] CRAN (R 4.1.1)
# labeling 0.4.2 2020-10-20 [1] CRAN (R 4.1.0)
# lattice 0.20-44 2021-05-02 [1] CRAN (R 4.1.1)
# lazyeval 0.2.2 2019-03-15 [1] CRAN (R 4.1.1)
# lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.1.1)
# magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.1.1)
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# munsell 0.5.0 2018-06-12 [1] CRAN (R 4.1.1)
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# patchwork * 1.1.1 2020-12-17 [1] CRAN (R 4.1.1)
# pillar 1.6.2 2021-07-29 [1] CRAN (R 4.1.1)
# pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.1.1)
# pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.1.1)
# pkgload 1.2.1 2021-04-06 [1] CRAN (R 4.1.1)
# plyr 1.8.6 2020-03-03 [1] CRAN (R 4.1.1)
# prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.1.1)
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# ps 1.6.0 2021-02-28 [1] CRAN (R 4.1.1)
# purrr 0.3.4 2020-04-17 [1] CRAN (R 4.1.1)
# R6 2.5.1 2021-08-19 [1] CRAN (R 4.1.1)
# Rcpp 1.0.7 2021-07-07 [1] CRAN (R 4.1.1)
# remotes 2.4.0 2021-06-02 [1] CRAN (R 4.1.1)
# reshape 0.8.8 2018-10-23 [1] CRAN (R 4.1.1)
# reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.1.1)
# rlang 0.4.11 2021-04-30 [1] CRAN (R 4.1.1)
# rmarkdown 2.10 2021-08-06 [1] CRAN (R 4.1.1)
# rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.1.1)
# rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.1.1)
# scales 1.1.1 2020-05-11 [1] CRAN (R 4.1.1)
# sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.1.1)
# stringi 1.7.4 2021-08-25 [1] CRAN (R 4.1.1)
# stringr 1.4.0 2019-02-10 [1] CRAN (R 4.1.1)
# testthat 3.0.4 2021-07-01 [1] CRAN (R 4.1.1)
# tibble 3.1.4 2021-08-25 [1] CRAN (R 4.1.1)
# tidyr 1.1.3 2021-03-03 [1] CRAN (R 4.1.1)
# tidyselect 1.1.1 2021-04-30 [1] CRAN (R 4.1.1)
# tidytree 0.3.4 2021-05-22 [1] CRAN (R 4.1.1)
# treeio * 1.16.2 2021-08-17 [1] Bioconductor
# usethis 2.0.1 2021-02-10 [1] CRAN (R 4.1.1)
# utf8 1.2.2 2021-07-24 [1] CRAN (R 4.1.1)
# vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.1.1)
# withr 2.4.2 2021-04-18 [1] CRAN (R 4.1.1)
# xfun 0.25 2021-08-06 [1] CRAN (R 4.1.1)
# yaml 2.2.1 2020-02-01 [1] CRAN (R 4.1.0)
# yulab.utils 0.0.2 2021-08-16 [1] CRAN (R 4.1.1)