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 *Z*_{C} and *n*̅_{H2O}.

First, load the `canprot`

package and data.

`library(canprot)`

Here we make plots for datasets for pancreatic cancer having a mean difference of *n*̅_{H2O} that is > 0.01 and a small *Z*_{C}, 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).