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 

## some frequently used HTML expressions
ZC <- "<i>Z</i><sub>C</sub>"

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

Dick JM, Yu M, Tan J, Lu A. 2019. Changes in carbon oxidation state of metagenomes along geochemical redox gradients. Frontiers in Microbiology 10: 120. doi: 10.3389/fmicb.2019.00120

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

library(JMDplots)

General characteristics of r ZC of DNA, RNA, and proteins (Figure 1)

gradox1()

Selected plots of metagenomic DNA, RNA, and protein r ZC (Figure 2)

gradox2()

All plots of DNA and RNA r ZC (Figure S1)

mout <- gradoxS1()

All plots of protein r ZC (Figure S2)

pout <- gradoxS2()

r ZC of proteins vs DNA (metagenomes and metatranscriptomes) (Figure 3)

gradox3(mout, pout)

Thermodynamic calculations of relative stabilities along redox gradients (Figure 4)

gradox4(mout, pout)

r ZC of reads classified to selected abundant species (Figure 5)

gradox5()

r ZC of reads classified to selected abundant species (including deeper samples) (Figure S3)

gradox5(maxdepth = NULL)

jedick/JMDplots documentation built on April 12, 2025, 1:35 p.m.