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 (R-Forge?)
if (!nzchar(Sys.which("pngquant"))) pngquant <- NULL 

This vignette from the R package JMDplots version r packageDescription("JMDplots")$Version shows chemical metrics for proteins coded by genes that are differentially expressed in hyperosmotic compared to control conditions. The analysis is described in more detail in a paper (Dick et al., 2020). Abbreviations:

• Z_C – average oxidation state of carbon.
• n_H2O – stoichiometric hydration state per residue (Dick et al., 2020) computed using the QEC basis species (glutamine, glutamic acid, cysteine, H~2~O, O~2~).
• pI – isoelectric point; GRAVY – grand average of hydropathicity.
• n_AA – protein length; MW – molecular weight per residue.

options(width = 90)

datasets <- pdat_osmotic_gene(2020)

pdat1 <- lapply(datasets, pdat_osmotic_gene)
comptab1 <- lapply(pdat1, get_comptab)
comptab2 <- lapply(pdat1, get_comptab, "pI", "GRAVY")
comptab3 <- lapply(pdat1, get_comptab, "nAA", "MW")

Differences are calculated as (median value for proteins coded by up-regulated genes) - (median value for proteins coded by down-regulated genes). Dashed lines enclose the 50% credible region for highest probability density.

layout(matrix(c(0, 2, 1, 2, 1, 3, 0, 3), nrow = 2))
par(cex = 1, mar = c(4, 4, 1, 1), mgp = c(2.5, 1, 0))
diffplot(comptab1, labtext = NA)
diffplot(comptab2, c("pI", "GRAVY"), labtext = NA)
diffplot(comptab3, c("nAA", "MW"), labtext = NA)

In the table, values of ΔZ_C, Δn_H2O, and ΔGRAVY are multiplied by 1000, values of ΔpI and ΔMW are multiplied by 100, and negative values are shown in bold. Abbreviations:

• n_down – number of down-regulated genes; n_up – number of up-regulated genes.

library(xtable)
out <- xsummary3(comptab1, comptab2, comptab3)
# round values and include dataset tags
tags <- sapply(sapply(strsplit(datasets, "="), "[", -1), paste, collapse = ";")
out <- cbind(out[, 1:2], tags = tags, out[, 3:19])
out[, 6:20] <- round(out[, 6:20], 4)
file <- paste0("osmotic_gene.csv")
write.csv(out, file, row.names = FALSE, quote = 2)

Data Sources

a. b. Tables 1--2 of @KSA+02. c. Table 1 of @WJ02. d. e. Table 3 of @HZP+05. f. Table 1S of @LGW+05. g. Tables 2--3 of @SLA+05. h. i. Dataset.txt of @GCP08. j. k. Table 3 of @SBB+09. l. Table S2 (sheet "S2_Table_3") of @HMO+10. m. n. o. p. Table S5 of @BBWB12, filtered to include genes with log~2~ fold change > 1 or < -1. q. Table S2 of @LB12, filtered to include genes with p-value < 0.05 and fold change > 2 or < 0.5. r. s. t. Supplementary Tables S2A--S2F of @QHT+13. u. v. Dataset.txt of @WGB+13, filtered to include proteins with log fold change (column "N vs K Wmean [M]" for NaCl and "U vs K Wmean [M]" for urea) > 1 or < 1 and p-value less than 0.05. w. Table S2 of @ADW+14 x. y. z. Table S2 of @KKG+14 A. B. Tables S5--S6 of @KSM+14. C. D. E. F. Supplemental Table S1 of @MGM+14, filtered to include genes with differences of Normalized ln(cDNA/gDNA) > 1 or < 1 between 2 % and higher NaCl concentration. G. H. I. Table S2 of @SLM+14. J. K. L. M. N. O. P. Q. R. Tables S1--S3 of @FRH+15. S. T. Table S2 of @KLB+15. U. V. Tables S5--S8 of @HLL17. W. Table S6 of @MWZ+18.

References

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