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