JMDplots vignettes

Carbon oxidation state of proteins inferred from metagenomes in redox gradients (2019)

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 2025-05-20 with JMDplots 1.2.22 and CHNOSZ 2.1.0-72.

library(JMDplots)

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

gradox1()

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

gradox2()

All plots of DNA and RNA ZC (Figure S1)

mout <- gradoxS1()

All plots of protein ZC (Figure S2)

pout <- gradoxS2()

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)

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

gradox5()

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

gradox5(maxdepth = NULL)