R/sbml2hyperdraw.R

In BiGGR: Constraint based modeling in R using metabolic reconstruction databases

sbml2hyperdraw <- function(sbml.model,
					   rates=NULL,
					   relevant.species=unname(sapply(sbml.model@species, id)),
					   relevant.reactions=unname(sapply(sbml.model@reactions, id)),
					   layoutType="dot", lwd.max=3, lwd.min=0.5, plt.margins=c(150, 150, 150, 150)){
##Build hyperedges from  SBML reactions
hyperedges <- unlist(sapply(sbml.model@reactions, function(r){
if(r@id %in% relevant.reactions){
  reactants <- intersect(sapply(r@reactants, species), relevant.species)
  products <- intersect(sapply(r@products, species), relevant.species)
  if (length(reactants)>0 & length(products)>0){
	##Change direction into direction of flux if rate is  < 0
	my.label <- ifelse(r@id %in% names(rates), paste(r@id, round(rates[r@id], 2), sep=":"), r@id)
	if (! is.null(rates) && rates[r@id]<0)
	  DirectedHyperedge(products, reactants, label=my.label)
	else      
	  DirectedHyperedge(reactants, products, label=my.label)
  }
}
}, simplify=TRUE))

##If rates are given, append them  to edge names
if(hasArg(rates)){
names(hyperedges) <- paste(names(hyperedges), ":", round(rates, 2)[names(hyperedges)], sep="")
names(rates) <- paste(names(rates), ":", round(rates, 2), sep="")
} else {
rates <- sapply(sbml.model@reactions, function(r)1) ##if no rates given, set them to one
}

##Build graph object
node.names <- unique(unlist(c(lapply(hyperedges, function(x)x@head), lapply(hyperedges, function(x)x@tail))))
hg <- Hypergraph(node.names, hyperedges)
testbph <- graphBPH(hg)
my.graph <- graphLayout(testbph, layoutType=layoutType)

nodeDataDefaults(my.graph, "shape") <- "box"
nodeDataDefaults(my.graph, "margin") <- 'unit(3, "mm")'  
edgeDataDefaults(my.graph, "lwd") <- 1
graphDataDefaults(my.graph, "arrowLoc") <- "end"

##calculate line widths from rates
lwds <- abs(rates[my.graph@edgeNodes]) / max(abs(rates[my.graph@edgeNodes])) * lwd.max
lwds[which(lwds<lwd.min)] <- lwd.min
for (rxn.id in names(rates)){
##set grey color for reaction edges with rate 0     
if (unname(rates[rxn.id])==0){
  lapply(my.graph@edgeNodeIO$outgoing[[rxn.id]], function(x)edgeData(my.graph, rxn.id, x, "color") <- "grey")
  lapply(my.graph@edgeNodeIO$incoming[[rxn.id]], function(x)edgeData(my.graph, x, rxn.id, "color") <- "grey")    
}
##set red color for reaction edges with rate < 0 
##also reverse direction of arrow for reactions edges with rate < 0
if (unname(rates[rxn.id])<0){
  lapply(my.graph@edgeNodeIO$outgoing[[rxn.id]], function(x)edgeData(my.graph, rxn.id, x, "color") <- "red")
  lapply(my.graph@edgeNodeIO$incoming[[rxn.id]], function(x)edgeData(my.graph, x, rxn.id, "color") <- "red")    
}

##Set line widths
lwd <- unname(ifelse(lwds[rxn.id]==2.8,  as.character(min(lwds)), as.character(lwds[rxn.id]))) ##set lwd to min lwd if rate is zero
lapply(my.graph@edgeNodeIO$outgoing[[rxn.id]], function(x)edgeData(my.graph, rxn.id, x, "lwd") <- as.character(lwds[rxn.id]))
lapply(my.graph@edgeNodeIO$incoming[[rxn.id]], function(x)edgeData(my.graph, x, rxn.id, "lwd") <- as.character(lwds[rxn.id]))
}

##Set plot margins
my.graph@graph@boundBox@botLeft@y <- my.graph@graph@boundBox@botLeft@y-plt.margins[1] ##bottom
my.graph@graph@boundBox@botLeft@x <- my.graph@graph@boundBox@botLeft@x-plt.margins[2] ##left 
my.graph@graph@boundBox@upRight@y <- my.graph@graph@boundBox@upRight@y+plt.margins[3] ##top
my.graph@graph@boundBox@upRight@x <- my.graph@graph@boundBox@upRight@x+plt.margins[4] ##right  
##  pushViewport(viewport(gp=gpar(cex=cex.lab)))

return(my.graph)
}