Awesome
Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers
If you use this work in published research, please cite:
S Xu<sup>#</sup>, M Chen<sup>#</sup>, T Feng, L Zhan, L Zhou, G Yu<sup>*</sup>. 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
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# 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)
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# 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)
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# 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)
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