In jedick/JMDplots: Plots from Papers by Jeffrey M. Dick

library(JMDplots)
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 that are differentially expressed in eukaryotic cells exposed to hyperosmotic stress, compared to control conditions. The analysis is described in more detail in a paper (Dick, 2021). 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~).

datasets <- pdat_osmotic_euk(2020)

pdat1 <- lapply(datasets, pdat_osmotic_euk)
comptab1 <- lapply(pdat1, get_comptab)
comptab2 <- lapply(pdat1, get_comptab, "nAA", "MW")

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

par(mar = c(4, 4, 1, 1))
diffplot(comptab1, labtext = NA)

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

• n~down~ – number of down-regulated proteins; n~up~ – number of up-regulated proteins; HTS – hypertonic saline; Cmx – cytomix treatment.
• n_AA – protein length; MW – molecular weight per residue.

library(xtable)
out <- xsummary2(comptab1, comptab2)
# round values and include dataset tags
tags <- sapply(sapply(strsplit(datasets, "="), "[", -1), paste, collapse = ";")
out <- cbind(out[, 1:2], tags = tags, out[, 3:16])
out[, 6:17] <- round(out[, 6:17], 4)
file <- paste0("osmotic_euk.csv")
write.csv(out, file, row.names = FALSE, quote = 2)

Data Sources

a. Tables II--III of @DAA+05. b. Table 1 of @MHN+08. c. d. e. f. g. Dataset S3 of @LTH+11, filtered to include proteins with q-value < 0.05, same direction of change in all 3 replicates for each condition, and median log fold change > 0.2. h. Supplementary Table 1 of @OBBH11. i. j. k. l. m. n. Supplementary Table S1 of @LFY+12 (sheet "All proteins"), filtered to include proteins with q-value < 0.1. o. Table 2 of @CLG+15. p. q. Supplemental Data S1 of @SCG+15 (file "ClusterGroup.AllProteins.051814.csv"), filtered to include proteins in clusters 1--4 (differential expression at all time points (1/4) or after > 20 min delay (2/3)). r. Table 1 of @YDZ+15. s. t. Supplementary Table 2 of @GAM+16, filtered to include proteins with fold change > 2 or < 0.5. u. Supplementary Tables 2 and 3 of @RBP+16. v. Supplementary Tables 1 and 2 of @JBG+18.

References

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