The goal of bppg is to provide functionality to create and characterize bipartite graphs that show the relationship between peptides and proteins in bottom-up proteomics. Functionality to use the bipartite graphs for protein quantification will be added in the future.
You can install the development version of bppg from GitHub with:
# install.packages("devtools")
devtools::install_github("mpc-bioinformatics/bppg")Example on how to plot a bipartite peptide-protein graph
library(bppg)
biadjacency_matrix <- matrix(c(1,1,1,0), nrow = 2)
G <- igraph::graph_from_incidence_matrix(biadjacency_matrix)
plotBipartiteGraph(G, three_shapes = TRUE, useCanonicalPermutation = TRUE)