Bio_draw_by_met

bio_draw_by_met(model, metAbbr, drawMap, radius, direction, excludeMets, flux, save, closev)[source]

bio_draw_by_met.m Script of the Paint4Net to define the scope of visualization by a metabolite USAGE: function [involvedRxns,involvedMets,deadEnds,deadRxns]=bio_draw_by_met(model,metAbbr,drawMap,radius,direction,excludeMets,flux,save,closev)

INPUTS:

model - COBRA Toolbox model metAbbr - a cell type variable that can take a value that represents the

abbreviation of a metabolite in the COBRA model. This metabolite is the start point for visualization.

OPTIONAL INPUT:

drawMap - a logical type variable that can take value of true or false

(default is false) indicating whether to visualize the COBRA model or not.

radius - a double type variable that can take a value of natural numbers

(1,2,3n). The argument radius indicates the depth of an analysis of the initial metabolite.

direction - a string type variable that can take value of ‘struc’, ‘sub’,

‘prod’ or ‘both’ (default is ‘struc’).

excludeMets - a list of metabolites (default is empty) that will be excluded

from the visualization map.

flux - a double type Nx1 size vector of fluxes of reactions where N is number

of reactions (default is empty, meaning no flux data provided).

save - a boolean type variable that can take value of true or false

(default is false) indicating whether to automatically save visualization as jpeg file or not.

closev - a boolean type variable that can take value of true or false

(default is false) indicating whether to close the biograph viewer window or not after the visualization.

OUTPUT

involvedRxns - a cell type vector that contains a list of the involved reactions. involvedMets - a cell type vector that contains a list of the involved metabolites. deadEnds - a cell type vector that contains a list of the dead end metabolites. deadRxns - a cell type vector that contains a list of dead end reactions.

..Author: -Andrejs Kostromins 04/10/2012 E-mail: andrejs.kostromins@gmail.com

bio_findNearRxns(model, Rxns, direction, flux)[source]

Finds neighbouring reactions for Paint4Net visualisation.

USAGE:

Rxns = findNearRxns (model, Rxns, direction, flux)

INPUTS:

  • model – COBRA model structure.

  • Rxns – Cell array of reaction abbreviations in the COBRA model, or a cell vector from the MATLAB workspace.

OPTIONAL INPUTS:

  • direction – Direction used by the algorithm. Allowed values are:

    • ‘struc’ - Visualise all metabolites connected to the specified reactions, without considering steady-state fluxes. This represents the structure of the COBRA model.

    • ‘sub’ - Visualise only metabolites acting as substrates for the specified reactions. Reaction direction is inferred from the stoichiometric matrix and steady-state fluxes.

    • ‘prod’ - Visualise only metabolites acting as products for the specified reactions. Reaction direction is inferred from the stoichiometric matrix and steady-state fluxes.

    • ‘both’ - Visualise both substrates and products for the specified reactions. Reaction direction is inferred from the stoichiometric matrix and steady-state fluxes.

    Default: ‘struc’

  • flux – nRxns x 1 vector of reaction fluxes, where nRxns is the number of reactions in the model. Fluxes are usually obtained with optimizeCbModel. Flux values smaller than -1e-9 mmol gDW^-1 h^-1 or greater than 1e-9 mmol gDW^-1 h^-1 are treated as non-zero.

    Default: vector of zeros.

OUTPUT:

Rxns – Cell array of neighbouring reaction abbreviations from the COBRA model.

Note

This function is an additional Paint4Net routine. It supports the draw_by_met command in Paint4Net v1.2, which calls draw_by_rxn and passes the direction argument.