Use ggbreak to effectively utilize plotting space to deal with large datasets and outliers
October 20, 2021 ยท View on GitHub
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
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# cli 3.0.1 2021-07-17 [1] CRAN (R 4.1.0)
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