inst/extdata/schoeberl.R

In robertness/pathflow: Converts biochemical reaction networks to pathway maps.

library(PathFlow)
library(signalgraph)
#data(schoeberl)
setwd("/Users/robertness/Dropbox/code/PathFlow")
load("data/schoeberl.Rdata")



g <- schoeberl.graph
V(g)[type == "species"]$type <- "place"
V(g)[type == "reaction"]$type <- "transition"
S <- getPetriNetMatrices(g)$S
pInvariants <- getMinimalInvariants(S)



tInvariants <- getMinimalInvariants(t(S))



"[EGFR]+[EGF]  ->  [EGF-EGFR]"



#nodes are the names of the pInvariants


influence.edges <- do.call("rbind", getOverlapEdges(pInvariants))
influence.edges <- c(influence.edges,
                     do.call("rbind", getConnectedEdges(pInvariants, tInvariants, g)))


Note there is no overlap.


pair

#if two pInvariants contain a place that is connected to another place that is in the tinvariants,
#draw an edge