MetabolicCartography¶

addColourNode(map, rxnList, colour)¶

Add colour to all metabolites linked to a list of reaction names. If no colour is specified as input, ‘RED’ will be used by default. Complementary function of changeRxnColorAndWidth.m

USAGE:

[map] = addColourNode(map, rxnList, color)

INPUTS:

map: A parsed model structure generated by: ‘transformXML2Map’ function

rxnlist: List of reactions which nodes have to be coloured

OPTIONAL INPUT:

color: Color string. Default color being ‘RED’

OUTPUT:

map: New parsed file with the colored entities linked: to reactions list given as input

addFluxFBA(map, model, fbaSolution, color)¶

Change reactions type for a specific list of reactions Visualize the fluxes obtained in a cobra model (FBA) in a CellDesigner map

USAGE:

[map2, flux3, fluxMap] = addFluxFBA(map, model, fbaSolution, rxnsColour)

INPUTS:

map: A parsed model structure generated by: ‘transformXML2Map’ function

model: A COBRA model fbaSolution: Structure obtain from flux balance analysis

OPTIONAL INPUT:

color: Add colour to the reactions carrying fluxes

OUTPUTS:

map2: New parsed file with the changes in the reactions flux: Fluxes and normalized fluxes through all rxns fluxMap: List of reactions carrying flux in the map + width value

addFluxFBAdirectionAndColor(map, model, fbaSolution)¶

Change reactions type for a specific list of reactions

USAGE:

[map, flux2, fluxMap] = addFluxFBAdirectionAndColor(map, model, fbaSolution)

INPUTS:

map: A parsed model structure generated by: ‘transformXML2Map’ function

model: A COBRA model fbaSolution: structure obtain from flux balance analysis

OUTPUTS:

map: mew parsed file with the changes in the reactions flux2: fluxes and normalized fluxes through all rxns fluxMap: list of reactions carrying flux in the map + width value

addNotes(model, map)¶

Function to add notes from a model to a metabolic map

USAGE:

[newMap] = addNotes(model, map)

INPUTS:: model: COBRA model map: A parsed model structure generated by

‘transformXML2Map’ function
OUTPUT:: newMap: Modified map containing notes from the model

changeMetColor(map, metList, color)¶

Change color of every metabolite from a list of Names

USAGE:

[newMap] = changeMetColor(map, metList, color);

INPUTS:: map: file from CellDesigner parsed to MATLAB format metList: List of metabolites names
OPTIONAL INPUT:: color: New color of metabolites from list(default: RED)
OUTPUT:: newMap: Matlab structure of map with reaction modifications

changeNodesArea(map, metList, areaHeight, areaWidth)¶

Change the area size of a list of metabolites (standardize the map)

USAGE:

[map2] = changeNodesArea(map,metList,areaHeight,areaWidth)

INPUTS:

map: A parsed model structure generated by: ‘transformXML2Map’ function

metList: list of metabolites which area wants to be changed

OPTIONAL INPUTS:

areaHeight: change heigt areaWidth: change areaWidth

OUTPUTS:

map2: New parsed file with the changes in the reactions

changeRxnColorAndWidth(map, rxnList, color, areaWidth)¶

Change color and areaWidth of reactions from a list of names

USAGE:

[newMap] = changeRxnColorAndareaWidth(map, rxnList, color, areaWidth);

INPUTS:: map: File from CellDesigner parsed to MATLAB format rxnList: List of reactions
OPTIONAL INPUTS:: color: New color of reactions from list (default: ‘RED’) areaWidth: New areaWidth of reactions from list (default: 8)
OUTPUT:: newMap: Matlab structure of map with reaction modifications

changeRxnType(map, rxnsList, rxnsType)¶

Change reactions type for a specific list of reactions. For example, pass from ‘STATE_TRANSITION’ to ‘TRANSPORT’.

USAGE:

[map2] = changeRxnType(map,listRxns,typeRxns)

INPUTS:

map: A parsed model structure generated by: ‘transformXML2Map’ function

rxnsList: List of reactions names want to be changed rxnsType: string (new reaction type)

OUTPUT:

map2: New parsed file with the changes in the reactions

checkCDerrors(map, model, printLevel, excelName)¶

Check discrepancies between a CD map and a COBRA model.

USAGE:

[rxn, met, rev, form] = checkCDerros(map, model)

INPUTS:

map: A parsed model structure generated by: ‘transformXML2Map’ function

model: A COBRA model

printLevel:

OUTPUTS:

rxn: structure with common reactions between map and model: extra reactions in map not in the model. extra reactions in the model not in the map.
met: structure with common mets in map and model: extra mets in map not in model. extra mets in model not in map.
rev: structure with: reversible reaction in map, considered irreversible in model. irreversible reaction in map, considered reversible in model.

form: structure with formula errors etc

colorProtein(map, protList, color)¶

Color protein nodes base on a list of protein Names

USAGE:

[newMap] = colorProtein(map, protList, color)

INPUTS:

map: xml file parsed to Matlab using the function: ‘transformFullXML2Map’

protList: List of protein names

OPTIONAL INPUT:

color: Color for the proteins in CAPITALS

OUTPUT:

newMap: Map with proteins nodes coloured (default: ‘RED’)

colorRxnType(map, type, color, width)¶

colors reactions based on their type and modifies their width.

USAGE:

[newMap] = createColorsMap(map, type, color);

INPUTS:

map: Map from CellDesigner parsed to MATLAB format type: Type of reactions to be colored (as String) color: Color used to color reactions (see createColorsMap.m) width: Width size for reactions (default: 8)

OUTPUT:

newMap: MATLAB structure of new map with needed reactions type: colored and width modified

colorRxnsFromGenes(map, model, entrezList, color, areaWidth)¶

Color and change the areaWidth of reactions based on the implicated gene given from a list of entezIDs.

USAGE:

[newmap] = colorRxnsFromGenes(map, model, entrezList, color, areaWidth);

INPUTS:

map: map from CellDesigner parsed to MATLAB format model: COBRA model entrezList: List of genes, given as entrezIDs.

OPTIONAL INPUTS:

color: Preferred color, as written in function: ‘createColorsMap’. (default: ‘RED’)

areaWidth: Preferred areaWidth of lines. (default: 8)

OUTPUT:

newmap MATLAB structure of new map with default look

colorSubsystemCD(map, model, subsystem, color, areaWidth)¶

Color and increase areaWidth of every reaction in a specific subsystem

USAGE:

[newMap] = colorSubsystemCD(map, model, subsystem, color, areaWidth);

INPUTS:: map: File from CellDesigner parsed to MATLAB format model: COBRA model structure subsystem: Name of a subsystem as a String
OPTIONAL INPUTS:: color: Color desired for reactions in CAPITALS areaWidth: Width desired for reactions
OUTPUT:: newMap MATLAB structure of map with reaction modifications

compareModelMapFormulas(model, map, excelName)¶

Checks the errors in a given map using a given base model by comparing the reactions formulas. As different errors can exist, the output is separated in 4 different tables that can later be exported into Excel spreadsheets (see commented lines at the end).

USAGE:

[wrongTable, absentModelTable, absentMapTable, duplicateTable] = compareModelMapFormulas(model, map, excelName)

INPUTS:

model: COBRA structure of a model map: MATLAB structure of the map obtained from the

function transformXML2Map.

OPTIONAL INPUT:

excelName: Name of the excel file in which to export the info

OUTPUTS:

wrongTable: Table containing the information on wrong

reactions. The fields are arranged as followed:

rxnName - Name of the reaction in the map

rxnID - ID of the reaction in the map

modelFormula - Formula of the reaction from the model

mapFormula - Formula of the reaction from the map

absentModelTable: Table containing the information on

reactions present in the map but absent from the model. The fields are arranged as followed:

rxnName - Name of the reaction in the map

rxnID - ID of the reaction in the map

mapFormula - Formula of the reaction from the map

absentMapTable: Table containing the information on

reactions present in the model but absent from the map. The fields are arranged as followed:

rxnName - Name of the reaction in the model

modelFormula - Formula of the reaction from the model

duplicateTable: Table containing the information on

duplicated reactions in the map. The fields are arranged as followed:

rxnName - Name of the reaction in the model

rxnID - ID of the reaction in the map

modelFormula - Formula of the reaction from the model

mapFormula - Formula of the reaction from the map

correctMetNameCD(map, metStructure, metList)¶

Correct the list of wrong metabolites names in the map obtained from checkCDerrors given a list of metabolites with the right names. Therefore, the wrong names in the map should become those of the model.

USAGE:

[map] = correctMetNameCD(map, metStructure, metList)

INPUTS:

map: A parsed model structure generated by: ‘transformXML2Map’ function

metStructure: Second OUTPUT obtained when running checkCDerrors metList: List of metabolites with right names

OUTPUT:

map: Corrected map

correctRxnNameCD(map, rxnStucture, rxnList)¶

Correct the list of wrong reaction names in the map obtained from checkCDerrors given a list of reaction with the right names. Therefore, the wrong names in the map should become those of the model.

USAGE:

[map] = correctRxnNameCD(map, rxnStucture, rxnList)

INPUTS:

map: A parsed model structure generated by: ‘transformXML2Map’ function

rxnStucture: First OUTPUT obtained when running checkCDerrors rxnList: list of reactions with right names

OUTPUT:

map: corrected map

createColorsMap()¶

Creates a Map type of structure storing colors by their name in capitals and giving their corresponding HTML color code.

USAGE:

[colors] = createColorsMap()

OUTPUTS:

colors: Map structure (similar to a dictionary) containing a: list of colors in the string format and giving the corresponding colors when called in the Map.

defaultColorCD(map)¶

Change all reaction lines to black and default areaWidth

USAGE:

[newmap] = defaultColorCD(map);

INPUT:

map: file from CellDesigner parsed to matlab format

OUTPUT:

newmap: MATLAB structure of map with all rxn lines as default: color and areaWidth

defaultLookMap(map)¶

Give default look to structures on map in terms of color, size and areaWidth.

USAGE:

[newmap] = defaultLookMap(map)

INPUT: map: Map from CellDesigner parsed to matlab format

OUTPUT:: newmap: MATLAB structure of new map with default look

Note

Note that this is specific to MitoMap and Recon3Map, as it uses Recon3 and PDmap nomenclature for metabolites

findMetsFromCompartInMap(map, compartment)¶

Finds all the metabolites and their names in the map structure for a compartment of interest.

USAGE:

[mets, id] = findMetFromCompartMap(map, Compartment)

INPUTS:: map: Map from CellDesigner parsed to matlab format compartment: Compartment of interest (e.g.: ‘[m]’,’[n]’,’[e]’,etc.)
OUTPUTS:: mets: List of metabolites names id: Metabolites indexes

findMetsInMap(map, metList)¶

Finds metabolites indices in a CellDesigner map for a given list of names

USAGE:

[metID] = findMetIdsMap(map, metList)

INPUTS:: map: Map from CellDesigner parsed to MATLAB format metList: List of metabolites names
OUTPUT:: metID: List of metabolite indices corresponding to metList

findRxnsFromCompartInMap(map, compartment)¶

Finds all the reactions and their names in the map structure for a compartment of interest.

USAGE:

[rxns, id] = findRxnFromCompartMap(map, Compartment)

INPUTS:: map: Map from CellDesigner parsed to matlab format compartment: Compartment of interest (e.g.: ‘[m]’,’[n]’,’[e]’,etc.)
OUTPUTS:: rxns: List of reaction names id: Reactions indexes

findRxnsInMap(map, rxnList)¶

Finds reaction indices in a CellDesigner map from a list of names

USAGE:

[rxnID, rxnIDref] = findRxnIDs(map, rxnList)

INPUTS:: map: Map from CellDesigner parsed to MATLAB format rxnList: List of reaction names
OUTPUTS:: rxnIDref: ID reference for reactions rxnID: List of reactions indices

findRxnsPerTypeInMap(map, rxnType)¶

Finds reaction names based on the type of reactions in the map. Useful to look for transport, catalysis or simple state_transition.

USAGE:

[listRxns] = findTransRxns(map, rxnType)

INPUTS:

map: Map from CellDesigner parsed to MATLAB format rxnType: Reaction type as a String

OUTPUT:

listRxns: List of reactions indexes (1st column) and: reaction names (2nd column)

getMapMatrices(map)¶

Adds 3 matrices to the map structure given as input.

USAGE:

[map] = getMapMatrices(map)

INPUT:

map: MATLAB structure of the map

sID - Stoichiometric matrix with rows = MetabolitesID and columns = ReactionsID in the same order as in the map structure. Contains -1 if the metabolite is a reactant/substract, +1 if the metabolite is a product and 0 if it does not participate in the reaction.

sAlias - Stoichiometric matrix with rows = MetabolitesAlias and columns = ReactionsID in the same order as in the map structure. Contains -1 if the metabolite is a reactant/substract, +1 if the metabolite is a product and 0 if it does not participate in the reaction.

idAlias - Logical matrix with rows = MetabolitesID and columns = MetabolitesAlias. Contains +1 if the MetaboliteID match with the MetaboliteAlias and 0 if it doesn’t.

OUTPUT:

map: Updated map structure from the input containing: the 3 matrices

mapFormula(map, rxnList)¶

Prints reactions formulas from a CellDesigner XML map file

USAGE:

[formulaList, rxnsList, absentRxns, duplicatedRxns] = mapFormula(map, rxnList)

INPUTS:

map: A parsed model structure generated by: “transformXML2Map” function

rxnList: List of reactions which formulas will to be printed

OUTPUTS:

formulaList: List of formulas rxnsList: Present reactions from the list (rxnList) in the map absentRxns: Reactions in the map not in the model duplicatedRxns: Duplicated reactions in the map

modifyReactionsMetabolites(map, rxnList, metList, newColor, newAreaWidth)¶

Modifies the color and areaWidth of reactions from a given list as input and the color of the corresponding metabolites from a given list as input. The colors and areaWidth are given as inputs and only metabolites present in the given reactions list will be colored.

USAGE:

[mapStruct] = modifyReactionsMetabolites(map, rxnList, metList, newColor, newAreaWidth)

INPUTS:

map: Matlab structure of the map obtained from the: function “transformXML2Map”.

rxnList: List of reaction names as a string array metList: List of metabolite names as a string array newColor: Color chosen for reaction lines and metabolites

given as a string with the corresponding real name. Possible names can be found in the function “createColorsMap.m”.

newAreaWidth: Width size for the reaction lines. Can be given as: a string or a double.

OUTPUT:

mapStruct: Updated map structure with the changed areaWidth and: color of the reactions and their corresponding metabolites.

removeCDReactions(fileName, rxnRemoveList, printLevel)¶

removes a list of reactions from a cell designer map, also removes correspinding species and species aliases if necessary

INPUT

xmlStruct: Structure obtained from the “xml2struct” function.
To be kept for the conversion back to an XML file of the structure.

map: Matlab structure of the map containing all the
relevant fields usable for checking and correction.

rxnRemoveList: Cell array of reaction abbreviation to be removed

printLevel: {0,(1)}

OUTPUT

xmlStructOut: Structure for the conversion back to an XML file
of the structure.

mapOut: Matlab structure of the smaller map containing all the
relevant fields usable for checking and correction.

rxnNotInMap: boolean vector the length of rxnRemoveList
indicating reactions that could not be found in the map

Ronan Fleming 2020

removeMapMol(xmlStruct, map, molRemoveList, printLevel)¶

removes a list of molecules (species alias) from a cell designer map, also removes corresponding reaction if necessary

INPUT

xmlStruct: Structure obtained from the “xml2struct” function.
To be kept for the conversion back to an XML file of the structure.

map: Matlab structure of the map containing all the
relevant fields usable for checking and correction.

molRemoveList: Cell array of molecule abbreviation to be removed

printLevel: {0,(1)}

OUTPUT

xmlStructOut: Structure for the conversion back to an XML file
of the structure.

mapOut: Matlab structure of the smaller map containing all the
relevant fields usable for checking and correction.

specNotInMap: boolean vector the length of molRemoveList
indicating species that could not be found in the map

Ronan Fleming 2020

removeMapReactions(xmlStruct, map, rxnRemoveList, printLevel)¶

removes a list of reactions from a cell designer map, also removes correspinding species and species aliases if necessary

INPUT

xmlStruct: Structure obtained from the “xml2struct” function.
To be kept for the conversion back to an XML file of the structure.

map: Matlab structure of the map containing all the
relevant fields usable for checking and correction.

rxnRemoveList: Cell array of reaction abbreviation to be removed

printLevel: {0,(1)}

OUTPUT

xmlStructOut: Structure for the conversion back to an XML file
of the structure.

mapOut: Matlab structure of the smaller map containing all the
relevant fields usable for checking and correction.

rxnNotInMap: boolean vector the length of rxnRemoveList
indicating reactions that could not be found in the map

Ronan Fleming 2020

removeMapSpecies(xmlStruct, map, specRemoveList, specRemoveType, printLevel)¶

removes a list of species from a cell designer map, also removes corresponding species aliases and reactions

INPUT

xmlStruct: Structure obtained from the “xml2struct” function.
To be kept for the conversion back to an XML file of the structure.

map: Matlab structure of the map containing all the
relevant fields usable for checking and correction.

specRemoveList: Cell array of species abbreviation to be removed

printLevel: {0,(1)}

OUTPUT

xmlStructOut: Structure for the conversion back to an XML file
of the structure.

mapOut: Matlab structure of the smaller map containing all the
relevant fields usable for checking and correction.

specNotInMap: boolean vector the length of specRemoveList
indicating species that could not be found in the map

Ronan Fleming 2020

removeMapSpeciesOnly(xmlStruct, map, specRemoveList, specRemoveType, printLevel)¶

removes a list of species from a cell designer map, also removes corresponding species aliases and but does not remove reactions

INPUT

xmlStruct: Structure obtained from the “xml2struct” function.
To be kept for the conversion back to an XML file of the structure.

map: Matlab structure of the map containing all the
relevant fields usable for checking and correction.

specRemoveList: Cell array of species abbreviation to be removed

printLevel: {0,(1)}

OUTPUT

xmlStruct: Structure for the conversion back to an XML file
of the structure.

map: Matlab structure of the smaller map containing all the
relevant fields usable for checking and correction.

specNotInMap: boolean vector the length of specRemoveList
indicating species that could not be found in the map

Ronan Fleming 2020

transformFullMap2XML(xmlStruct, map, fileName)¶

Creates a new XML file from the information contained in the map structure. Uses the function “struct2xml” to transform a matlab structure into an XML text format.

USAGE:

transformFullMap2XML(xmlStruct, map, fileName)

INPUTS:

xmlStruct: XML structure obtained from the function: “xml2struct”. Used by the function “struct2xml” to obtain the XML file.
map: Matlab structure of the map with the relevant: information. This information is then transfered to the xmlStruct for the conversion.

fileName: Path and name of the new XML file.

transformFullXML2Map(fileName)¶

Create a MATLAB structure from a given XML file. The XML file is first parsed through the “xml2struct” function and then transformed into a structure. The content of this structure can be found in the [description document](https://github.com/opencobra/cobratoolbox/blob/master/docs/source/notes/fullMATLABStructure.md)

USAGE:

[xmlStruct, map] = transformFullXML2Map(fileName)

INPUT:

fileName: Path to the XML file.

OUTPUTS:

xmlStruct: Structure obtained from the “xml2struct” function.: To be kept for the conversion back to an XML file of the structure.
map: Matlab structure of the map containing all the: relevant fields usable for checking and correction.

transformMap2XML(xmlStruct, map, fileName)¶

Creates a new XML file from the information contained in the map structure. Uses the function “struct2xml” to transform a matlab structure into an XML text format.

USAGE:

transformMap2XML(xmlStruct, map, fileName)

INPUTS:

xmlStruct: XML structure obtained from the function: “xml2struct”. Used by the function “struct2xml” to obtain the XML file.
map: Matlab structure of the map with the relevant: information. This information is then transfered to the xmlStruct for the conversion.

fileName: Path and name of the new XML file.

transformToIrreversibleMap(map, rxnlist)¶

Converts a map structure from irreversible format to reversible format for a list of reaction names

USAGE:

[mapIrrev] = transformToIrreversibleMap(map, rxnlist)

INPUTS:: map: Map from CellDesigner parsed to MATLAB format rxnlist: List of reaction names to transform
OUTPUT:: mapIrrev: Map with reactions in irreversible format

transformToReversibleMap(map, rxnlist)¶

Converts a map structure from irreversible format to reversible format for a list of reaction names

USAGE:

[mapRev] = transformToReversibleMap(map, rxnlist)

INPUTS:: map: Map from CellDesigner parsed to MATLAB format rxnlist: List of reaction names to transform
OUTPUT:: mapRev: Map in reversible format

transformXML2Map(fileName)¶

Create a MATLAB structure from a given XML file. The XML file is first parsed through the “xml2struct” function and then transformed into a structure. The content of this structure can be found in the [description document](https://github.com/opencobra/cobratoolbox/blob/master/docs/source/notes/simpleMATLABStructure.md)

USAGE:

[xmlStruct, map] = transformXML2Map(fileName)

INPUT:

fileName: Path to the XML file.

OUTPUTS:

xmlStruct: Structure obtained from the “xml2struct” function.

To be kept for the conversion back to an XML file of the structure.

map: Matlab structure of the map containing all the

relevant fields usable for checking and correction.

sID - Stoichiometric matrix with rows = MetabolitesID and columns = ReactionsID in the same order as in the map structure. Contains -1 if the metabolite is a reactant/substract, +1 if the metabolite is a product and 0 if it does not participate in the reaction.
sAlias - Stoichiometric matrix with rows = MetabolitesAlias and columns = ReactionsID in the same order as in the map structure. Contains -1 if the metabolite is a reactant/substract, +1 if the metabolite is a product and 0 if it does not participate in the reaction.
idAlias - Logical matrix with rows = MetabolitesID and columns = MetabolitesAlias. Contains +1 if the MetaboliteID match with the MetaboliteAlias and 0 if it doesn’t.

unifyMetabolicMapCD(map)¶

Unify colours in a metabolic map as a standard. Reaction will be grey and Metabolites will be White.

USAGE:

[map2] = unifyMetabolicMapCD(map)

INPUT:: map: MATLAB structure of CellDesigner map
OUTPUT:: map2: Map with grey reactions colour, width 1 and white nodes colour.

unifyMetabolicPPImapCD(map)¶

Unify a metabolic and protein-protein interaction map as a standard. Reaction will be grey and Metabolites/Complexes will be White.

USAGE:

[map2] = unifyMetabolicPPImapCD(map)

INPUT:

map: MATLAB structure of CellDesigner map

OUTPUT:

map2: Map with grey reactions colour, width 1 and white nodes colour.: Change colour complex to white