rodeo (version 0.7.6)

plotStoichiometry: Plot Qualitative Stoichiometry Matrix

Description

Visualizes the stoichiometry matrix using standard plot methods. The sign of stoichiometric factors is displayed as upward and downward pointing triangles, optionally colored.

Arguments

box

A vector of positive integers pointing to a spatial sub-unit of the model.

time

Time. The value is ignored in the case of autonomous models.

cex

Character expansion factor.

colPositive

Color for positive stoichiometric factors.

colNegative

Color for negative stoichiometric factors.

colGrid

Color of a grid (can be identical to background color).

See Also

See other methods of the rodeo-class or stoichiometry for computing the stoichiometric factors only. Alternative options for displaying stoichiometry information are described in the package vignette.

Examples

# NOT RUN {
data(vars, pars, funs, pros, stoi)
model <- rodeo$new(vars, pars, funs, pros, stoi, dim=c(1))
model$setVars(c(bac=0.1, sub=0.5))
model$setPars(c(mu=0.8, half=0.1, yield= 0.1, vol=1000, flow=50, sub_in=1))
monod <- function(c,h) {c/(c+h)}
model$plotStoichiometry(box=c(1))
# }