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 

options(width = 40)

## some frequently used HTML expressions
ZC <- "<i>Z</i><sub>C</sub>"
nH2O <- "<i>n</i>H<sub>2</sub>O"

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

Dick JM, Yu M, Tan J. 2020. Uncovering chemical signatures of salinity gradients through compositional analysis of protein sequences. Biogeosciences 17(23): 6145--6162. doi: 10.5194/bg-17-6145-2020

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

# Get RefSeq version 20210527
file <- system.file("extdata/RefSeq/README.txt", package = "chem16S")
release <- substr(strsplit(readLines(file, n=2)[2], "release ")[[1]][2], 1, 3)

For Figure 3, the RefSeq database release r release is used for the proteomes of nif-bearing organisms (release 201 was used in the paper).

library(JMDplots)

The QEC basis species (glutamine, glutamic acid, cysteine, H~2~O, O~2~) are used for the analysis of stoichiometric hydration state (r nH2O).

Number of reactions for each amino acid in E. coli metabolic reconstruction

Reaction equations used for this calculation are from Feist et al. (2007).

gradH2O0()

Comparison of different sets of basis species (Figure 1)

gradH2O1()

Schematic of r nH2O and r ZC calculations (Figure 2)

gradH2O2()

r nH2O-r ZC scatterplots for redox gradients and the Baltic Sea (Figure 3)

gradH2O3()

Data sources: Bison Pool [BP; @HRM+11; @SMS+12]; diffuse submarine vents [DV; @RRM+16; @FLBH18]; Guerrero Negro microbial mat [GN; @KRH+08]; nitrogenase-bearing organisms [NF; @PCF+18]; Baltic Sea [@DLY+14].

r nH2O for Baltic Sea metagenome and metatranscriptome in different size fractions (Figure 4)

gradH2O4()

Data sources: metagenome [@DLY+14] and metatranscriptome [@ASD+16].

r nH2O-r ZC for freshwater, marine, and hypersaline environments (Figure 5)

gradH2O5()

Data sources: Amazon river [@SFD+15] and plume [@SZD+14]; freshwater and marine metagenomes [@EZM+14]; hypersaline datasets Kulunda Steppe [KS; @VGR+16], Santa Pola [SP; @GPF+11; @FGM+13], San Francisco South Bay [SB; @KBW+18].

r nH2O-r ZC and GRAVY-pI plots for Baltic Sea and Rodriguez-Brito et al. data (Figure 6)

gradH2O6()

Data sources: @DLY+14 and @RLW+10.

Differential gene and protein expression; time-course experiments and NaCl or organic solutes (Figure 7)

gradH2O7()

Data sources: Panel (a): a--c: @KKG+14; d--f: @SLM+14; g--i: @FRH+15; j--k: @HLL17; l--n: @QHT+13. Panel (b): A--B: @KSA+02; C--D: @HZP+05; E--F: @KLB+15; G--J: @FRH+15; K--L: @SBB+09; M--N: @WGB+13. Panels (c) to (f): See the vignettes JMDplots::mkvig("osmotic_bact") and JMDplots::mkvig("osmotic_halo"). Links to static vignettes: osmotic_bact and osmotic_halo.

References

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