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 

## colorize messages 20171031
## adapted from https://gist.github.com/yihui/2629886#file-knitr-color-msg-rnw
color_block = function(color) {
  function(x, options) sprintf('<pre style="color:%s">%s</pre>', color, x)
}
knit_hooks$set(warning = color_block('magenta'), error = color_block('red'), message = color_block('blue'))

options(width = 80)

ZC <- "<i>Z</i><sub>C</sub>"

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

Dick JM, Shock EL. 2021. The release of energy during protein synthesis at ultramafic-hosted submarine hydrothermal ecosystems. Journal of Geophysical Research: Biogeosciences 126(11): e2021JG006436. doi: 10.1029/2021JG006436

Click here for full-text access to a view-only version of the paper.

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

library(JMDplots)

Affinities for methanogenesis and amino acid synthesis (Figure 1)

mjenergy1()

Calculations shown in this and other figures use activities of CH~4~, CO~2~, NH~4~^+^, H~2~S, H~2~, and H^+^ from the mixing models of @SC10.

r ZC of amino acids vs frequency in the Mj proteome (Figure 2)

mjenergy2()

Affinities of overall synthesis of proteins in the Mj proteome (Figure 3)

mjenergy3()

Calculate affinity for amino acid synthesis and polymerization

calc_affinity()

References

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