library(PathFlow) library(igraph) #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
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