plotStoichiometry: Plot Qualitative Stoichiometry Matrix

In rodeo: A Code Generator for ODE-Based Models

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.
shade	Logical. If TRUE, the dependence of process rates on state variables is indicated by shading.
colPositive	Color for positive stoichiometric factors.
colNegative	Color for negative stoichiometric factors.
colGrid	Color of a grid (can be identical to background color).
colShade	Shading color, if used.

Note

The values of state variables and parameters must have been set using the setVars and setPars methods. If the stoichiometric factors are mathematical expressions involving function references, these functions must be defined in R (even if the numerical computations are based on generated Fortran code).

Author(s)

[e-mail]

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

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))

Example output

rodeo documentation built on March 28, 2021, 1:09 a.m.