In jedick/JMDplots: Plots from Papers by Jeffrey M. Dick

library(knitr)
## use pngquant to reduce size of PNG images
knit_hooks$set(pngquant = hook_pngquant)
pngquant <- "--speed=1 --quality=0-25"
# in case pngquant isn't available
if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL

options(width = 80)

nH2O <- "<i>n</i><sub>H<sub>2</sub>O</sub>"
nO2 <- "<i>n</i><sub>O<sub>2</sub></sub>"

This vignette runs the code to make the plots from the following paper:

Dick JM, Kang X. 2023. chem16S: community-level chemical metrics for exploring genomic adaptation to environments. Bioinformatics 39(9): btad564. doi: 10.1093/bioinformatics/btad564

Update (2024-11-21): The figure has been updated to use GTDB release 220 for reference proteomes and taxonomic classification of the mouse dataset.

This vignette was compiled on r Sys.Date() with JMDplots r packageDescription("JMDplots")$Version and chem16S r packageDescription("chem16S")$Version.

library(JMDplots)

Code example and plots (Figure 1)

chem16S_1()

Data sources: The GlobalPatterns dataset is from the phyloseq package [@MH13] and is adapted from @CLW+11. The mouse gut dataset was created by analyzing sequence data from @SSZ+12 (downloaded here and used in the mothur MiSeq SOP and DADA2 Pipeline Tutorial) with the DADA2 pipeline modified to use 16S rRNA sequences from GTDB release 220 [@Ali24] for taxonomic classifications.