optsol_phpp-class: Class '"optsol_phpp"'

In sybil: Efficient Constrained Based Modelling

Description

Structure of the class "optsol_robAna". Objects of that class are returned by the function phpp.

Objects from the Class

Objects can be created by calls of the form new("optsol_phpp", ...).

Slots

ctrlflm:

Object of class "matrix" containing the control flux values.

redCosts:

Object of class "matrix" containing the reduced costs of the two control flux values.

ctrlr:

Object of class "reactId" containing the reaction id of the control reaction.

ctrlfl:

Object of class "numeric" unused, see ctrlflm.

preProc:

Object of class "ppProc" containing the results of pre-processing. See also optimizeProb.

postProc:

Object of class "ppProc" containing the results of post-processing. See also optimizeProb.

mod_id:

Object of class "character" containing the model id of the used model.

mod_key:

Object of class "character" containing the model key of the used model.

solver:

Object of class "character" indicating the used solver.

method:

Object of class "character" indicating the used method.

algorithm:

Object of class "character" containing the name of the algorithm used for optimizations.

num_of_prob:

Object of class "integer" indicating the number of optimization problems.

lp_num_cols:

Object of class "integer" indicating the number of columns.

lp_num_rows:

Object of class "integer" indicating the number of rows.

lp_obj:

Object of class "numeric" containing the optimal values of the objective function after optimization. If no flux distribution is available, slot lp_obj contains the cross-product of the objective coefficients in slot obj_coef and the part of the flux distribution in slot fluxdist containing the values representing fluxes in the entire metabolic network (slot fldind).

lp_ok:

Object of class "integer" containing the exit code of the optimization.

lp_stat:

Object of class "integer" containing the solution status of the optimization.

lp_dir:

Object of class "character" indicating the direction of optimization.

obj_coef:

Object of class "numeric" containing the objective coefficients of the used model (slot obj_coef of an object of class modelorg). These are not necessarily the objective coefficients of the used algorithm.

obj_func:

Object of class "character" containing the objective function of the used model. Usually, it contains the return value of printObjFunc.

fldind:

Object of class "integer" pointers to columns (variables) representing a flux (reaction) in the original network. The variable fldind[i] in the problem object represents reaction i in the original network.

fluxdist:

Object of class "fluxDistribution" containing the solutions flux distributions.

alg_par:

Object of class "list" containing a named list containing algorithm specific parameters.

Extends

Class "optsol_robAna", directly. Class "optsol_optimizeProb", by class "optsol_robAna", distance 2. Class "optsol", by class "optsol_robAna", distance 3.

Methods

ctrlfl

signature(object = "optsol_phpp"): gets the ctrlflm slot.

ctrlfl<-

signature(object = "optsol_phpp"): sets the ctrlflm slot.

getRedCosts

signature(lp = "optsol_phpp"): gets the ctrlflm slot.

plot

signature(x = "optsol_phpp", y = "character"): (main = paste("Reduced Costs:", y), xlab = react_id(ctrlr(x)[1]), ylab = react_id(ctrlr(x)[2]), shrink = c(0.95, 0.95), col.regions = colorRampPalette(c("#FFFFFF", "#F0F0F0", "#D9D9D9", "#BDBDBD", "#969696", "#737373", "#525252", "#252525", "#000000"))(100), ...):
plots the reduced costs of the control fluxes as levelplot.

y

reaction id of one control reaction.

main

plot title, see also levelplot.

xlab

label of x-axis, see also levelplot.

ylab

label of y-axis, see also levelplot.

shrink

scale of rectangles to plot, see levelplot.

col.regions

a vector of colors (default greyscale) see levelplot.

...

further graphical parameters to the levelplot function.

plot

signature(x = "optsol_phpp", y = "missing"): (xlab = list(label = react_id(ctrlr(x)[1]), rot = 30, cex = 0.8), ylab = list(label = react_id(ctrlr(x)[2]), rot = -40, cex = 0.8), zlab = list(label = obj_func(x), rot = 90, cex = 0.8), scales = list(arrows = FALSE, cex = 0.6, font = 3, tck = 1, col = "black"), par.settings = list(axis.line = list(col = "transparent")), shade = TRUE, shade.colors = function(irr, ref, height, w = 0.75) { grey(w * irr + (1 - w) * (1-(1-ref)^0.75)) }, ...):
plots the optimal values of the objective function vs. the control flux values in a wireframe plot.

xlab

label of x-axis, see also wireframe.

ylab

label of y-axis, see also wireframe.

zlab

label of z-axis, see also wireframe.

scales

parameters describing scales, see wireframe.

par.settings

additional parameters, see wireframe.

shade

enable/disable shading, see wireframe.

shade.colors

a function for the shading color (default greyscale), see wireframe.

...

further graphical parameters to the wireframe function.

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

See Also

phpp, checkOptSol and optsol

Examples

  showClass("optsol_phpp")

sybil documentation built on May 31, 2021, 5:08 p.m.