optsol_robAna-class: Class '"optsol_robAna"'

In sybil: Efficient Constrained Based Modelling

Description

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

Objects from the Class

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

Slots

ctrlr:

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

ctrlfl:

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

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_optimizeProb", directly. Class "optsol", by class "optsol_optimizeProb", distance 2.

Methods

ctrlfl:

signature(object = "optsol_robAna"): gets the ctrlfl slot.

ctrlfl<-:

signature(object = "optsol_robAna"): sets the ctrlfl slot.

ctrlr:

signature(object = "optsol_robAna"): gets the ctrlr slot.

ctrlr<-:

signature(object = "optsol_robAna"): sets the ctrlr slot.

plot

signature(x = "optsol_robAna", y = "missing") (xlab = paste("Control Flux:", react_id(ctrlr(x))), ylab = paste("Objective Function:", obj_func(x)), type = "b", pch = 20, fillColorBg = "grey", fillBg = TRUE, absCtrl = TRUE, ...):
plots the optimal values of the objective function vs. the control flux values.

xlab

label of x-axis, see also par.

ylab

label of y-axis, see also par.

type

plot type, see also par.

pch

how to plot the points, see also par.

fillColorBg

color of the area below the curve.

fillBg

logical: color the area below the curve.

absCtrl

if set to TRUE, the control flux values (x axis) are plotted as absolute values.

...

further graphical parameters to the points function.

Author(s)

Gabriel Gelius-Dietrich <[e-mail]>

Maintainer: Mayo Roettger <[e-mail]>

See Also

robAna, checkOptSol and optsol

Examples

  showClass("optsol_robAna")

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