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"
nO2 <- "<i>n</i>O<sub>2</sub>"

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

Dick JM. 2021. Water as a reactant in the differential expression of proteins in cancer. Computational & Systems Oncology 1(1): e1007. doi: 10.1002/cso2.1007

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

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).

Study overview (Figure 1)

canH2O1()

Median differences of r nH2O and r Zc for cell culture and cancer tissue (Figure 2)

canH2O2()

r nH2O-r Zc plots for TCGA and HPA datasets (Figure 3)

canH2O3()

Differentially expressed genes in aneuploid and osmotically shocked yeast cells (Figure 4)

canH2O4()

Mean differences and p-values for all datasets in each condition (Table 2)

Mean differences are followed by log~10~ of p-value in parentheses. Mean differences are computed as (mean of median values for up-regulated proteins in each dataset) - (mean of median values for down-regulated proteins in each dataset). The rows labelled "up" and "down" refer to (mean of median values for [up- or down-]regulated proteins in secreted proteins in hypoxia) - (mean of median values for [up-or down-]regulated proteins in whole-cell extracts in hypoxia).

kable(canH2OT2(), align = "r")

Supplementary Tables and Figures

Stoichiometric matrix for amino acids with QEC basis species (Table S1)

kable(canH2OT1())

r nO2-r Zc and r nH2O-r Zc correlations using QEC basis species (Figure S1)

canH2OS1()

HPA-TCGA scatterplots for r Zc and r nH2O (Figure S2)

canH2OS2()

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