sbml2hyperdraw: Returns a graph representation of an SBML model
In BiGGR: Constraint based modeling in R using metabolic reconstruction databases

Description Usage Arguments Value Author(s) See Also Examples

Convert an SBML model to a RagraphBPH using hypergraph. Metabolites are displayed as nodes and reactions are displayed as directed edges connecting the nodes. If a vector of rates is given, edge widths are weighted according to the rates. For negative rates, edges are drawn in red and the arrow between the metabolites is reversed to represent the correct direction of the flux.

1 2	sbml2hyperdraw(sbml.model, rates ,relevant.species, relevant.reactions,layoutType, lwd.max, lwd.min, plt.margins)

`sbml.model`	an rsbml `Model` object
`rates`	a named `vector` with the rates of the reactions in the model. The names of the rates must agree with the reaction identifiers in the sbml.model
`relevant.species`	a `vector` of type `character` defining a subset of species in the sbml.model to be plotted. Defaults to all species identifiers in the sbml.model.
`relevant.reactions`	a `vector` of type `character` defining a subset of reactions in the sbml.model to be plotted. Defaults to all reactions identifiers in the sbml.model.
`layoutType`	is a character string representing the layout engine to be used for visualization. Current supported layouts are "dot", "twopi","neato","fdp","sfdp" and "circo". Defaults to "dot". See `?GraphvizLayouts` for further documentation.
`lwd.max`	a `numeric` given the maximum edge width. Defaults to 3.
`lwd.min`	a `numeric` given the minimum edge width. Defaults to 0.5.
`plt.margins`	A numerical vector of the form c(bottom, left, top, right) giving additional white space around the graph (in case long node or edge labels fall outside the plotting region). Defaults to c(150,150,150,150).

Object of class RagraphBPH with the hypergraph representation of the SBML object.

Hannes Hettling <j.hettling@vu.nl>, Anand K. Gavai <anand.gavai@bioinformatics.nl>

RagraphBPH hyperdraw

##Generate an example model
path <- system.file("extdata", "Glycolysis_TCA_recon2_reactionIDs.txt", package="BiGGR")
reaction.ids <- scan(path, what=" ")

data("Recon2")
model <- buildSBMLFromReactionIDs(reaction.ids, Recon2)

##Plot ATP and ADP in cytosol and mitochondrion in model without rates
rel.sp <- c("M_adp_c", "M_atp_c", "M_adp_m", "M_atp_m")
hd <- sbml2hyperdraw(model, relevant.species=rel.sp)
plot(hd)

##Plot model with random rates
rates <- rnorm(length(model@reactions))
names(rates) <- sapply(model@reactions, id)
hd <- sbml2hyperdraw(model, rates=rates, relevant.species=rel.sp, lwd.max=4)
plot(hd)