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
pKa <- "p<i>K</i><sub>a</sub>"

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

Dick JM, LaRowe DE, Helgeson HC. 2006. Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins. Biogeosciences 3(3): 311–-336. doi: 10.5194/bg-3-311-2006

These plots have been modified from the original figures to add a neutral pH line to Figure 4 and a legend and colored labels to Figure 13.

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

library(JMDplots)

`r pKa` of sidechain and amino acid backbone groups (Figure 4)

aaaq4()

Net charge of proteins as a function of pH and T (Figure 10)

aaaq10()

Experimental data are from @RT71, @NT67, and @WG00.

Eh-pH diagram for extracellular α-amylases (Figure 13)

This plot, showing the relative stabilities of extracellular α-amylases from two organisms on an Eh-pH diagram, is based on Fig. 13 of Dick et al. (2006). Points are added for Eh-pH values from soils [@BKM60] and hot springs in Yellowstone [@SWM+05] and Iceland [@SA02]. Note that the symbols for Yellowstone and Iceland were incorrectly swapped in the original figure caption.