sbml2hyperdraw: Returns a graph representation of an SBML model

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

Description

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.

Usage

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

Arguments

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).

Value

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

Author(s)

Hannes Hettling <[e-mail]>, Anand K. Gavai <[e-mail]>

See Also

RagraphBPH hyperdraw

Examples

##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)

hettling/BiGGR documentation built on April 17, 2020, 5:19 a.m.