Bio_draw_by_met

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

Defines the visualisation scope from a starting metabolite (Paint4Net).

USAGE:

[involvedRxns, involvedMets, deadEnds, deadRxns] = bio_draw_by_met (model, metAbbr, drawMap, radius, direction, excludeMets, flux, save, closev)

INPUTS:

• model – COBRA model structure with fields:

  • .S - m x n stoichiometric matrix

• metAbbr – Cell array containing the abbreviation of a metabolite in the COBRA model. This metabolite is the starting point for visualisation.

OPTIONAL INPUTS:

• drawMap – Logical indicating whether to visualise the COBRA model.

  Default: false

• radius – Positive integer (1, 2, 3, …) defining the search depth from metAbbr.

  Default: 1

• direction – Direction used by the algorithm. Allowed values are struc, sub, prod, or both.

  Default: ‘struc’

• excludeMets – Cell array of metabolite abbreviations to exclude from the visualisation map.

  Default: empty

• flux – nRxns x 1 vector of reaction fluxes, where nRxns is the number of reactions in the model.

  Default: empty (no flux data provided)

• save – Boolean indicating whether to save the visualisation automatically as a JPEG file.

  Default: false

• closev – Boolean indicating whether to close the biograph viewer window after visualisation.

  Default: false

OUTPUTS:

• involvedRxns – Cell array containing the list of involved reactions.

• involvedMets – Cell array containing the list of involved metabolites.

• deadEnds – Cell array containing the list of dead-end metabolites.

• deadRxns – Cell array containing the list of dead-end reactions.

bio_findNearRxns(model, Rxns, direction, flux)

Finds neighbouring reactions for Paint4Net visualisation.

USAGE:

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

INPUTS:

• model – COBRA model structure with fields:

  • .S - m x n stoichiometric matrix

  • .mets - m x 1 cell array of metabolite identifiers

• 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.