plotStoichiometry {rodeo} | R Documentation |
Visualizes the stoichiometry matrix using standard plot methods. The sign of stoichiometric factors is displayed as upward and downward pointing triangles, optionally colored.
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). |
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).
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.
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))