plotStoichiometry: Plot Qualitative Stoichiometry Matrix

In dkneis/rodeo: A Code Generator for ODE-Based Models

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. Also visualized are dependencies of process rates on variables.

Arguments

box	A positive integer 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.
colInteract	Color used to highlight dependencies.
colBack	Color of background.
colGrid	Color of a grid.
lwdGrid	Grid line width.
translateVars	Optional function to recode variable labels. Must take the original vector as argument and return the altered version.
translatePros	Optional function to recode process labels. Must take the original vector as argument and return the altered version.

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))

dkneis/rodeo documentation built on Dec. 11, 2024, 12:20 p.m.