This vignette from the R package canprot demonstrates the calculation of potential diagrams for a group of datasets and generation of a merged diagram. Specifically, the potential diagrams show the weighted rank difference of chemical affinities between up- and down-expressed proteins in each dataset. Groups of datasets are considered that have similar compositional features, i.e. changes in ZC and n̅H2O.
First, load the canprot package and data.
library(canprot)Here we make plots for datasets for pancreatic cancer having a mean difference of n̅H2O that is > 0.01 and a small ZC, as judged by the p-value and CLES. Red and blue correspond to greater potential for formation of the up- and down-expressed proteins, respectively; the line of equipotential is shown in white:
gpresult <- groupplots("pancreatic_H2O_up", res = 25)
Now let’s make a merged diagram. The red-white-blue shading is computed from the mean of the previous diagrams. The black lines show the median and quartiles for the y-positions of the equipotential lines in the previous diagrams.
mergedplot(gpresult, res = 25)
Higher-resolution versions of these plots have been published in Figure S3 and Figure 3 of Dick, 2017 (Chemical composition and the potential for proteomic transformation in cancer, hypoxia, and hyperosmotic stress. PeerJ 5:e3421).