plotStoichiometry {rodeo} | R Documentation |
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)
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))