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
H2O <- "H<sub>2</sub>O"

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

Dick JM. 2009. Calculation of the relative metastabilities of proteins in subcellular compartments of Saccharomyces cerevisiae. BMC Systems Biology 3: 75. doi: 10.1186/1752-0509-3-75

These plots have been modified from the original figures to make greater use of color.

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

library(JMDplots)

Oxygen fugacity - activity of r H2O predominance diagrams (Figure 2)

scsc2()

Relative equilibrium abundances of proteins as a function of oxygen fugacity (Figure 3)

scsc3()

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