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>"
Topt <- "<i>T</i><sub>opt</sub>"

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

Dick JM. 2014. Average oxidation state of carbon in proteins. Journal of the Royal Society Interface 11: 20131095. doi: 10.1098/rsif.2013.1095

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

library(JMDplots)

r ZC of amino acids vs r ZC of RNA codons and hydropathy index of amino acids (Figure 1)

aoscp1()

Histograms of r ZC of all human proteins and human membrane proteins (Figure 2)

aoscp2()

Drawing of yeast cell color-coded with median r ZC of proteins in different locations (Figure 3)

# first make the base plot, then add labels
aoscp3(TRUE)
aoscp3()

r ZC and Eh ranges in yeast and ER-cytoplasm electron-transfer scheme (Figure 4)

aoscp4()

Average oxidation state of carbon in proteins from different organisms (Figure 5)

aoscp5()

r ZC and r Topt of different rubiscos and thermodynamic comparison (Figure 6)

aoscp6()

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