MetabolicCartography¶
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addColourNode
(map, rxnList, colour)[source]¶ 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
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addFluxFBA
(map, model, fbaSolution, color)[source]¶ 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
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addFluxFBAdirectionAndColor
(map, model, fbaSolution)[source]¶ 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
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addNotes
(model, map)[source]¶ 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
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changeMetColor
(map, metList, color)[source]¶ 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
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changeNodesArea
(map, metList, areaHeight, areaWidth)[source]¶ 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
Output
- map2 – New parsed file with the changes in the reactions
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changeRxnColorAndWidth
(map, rxnList, color, areaWidth)[source]¶ 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
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changeRxnType
(map, rxnsList, rxnsType)[source]¶ 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
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checkCDerrors
(map, model)[source]¶ 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
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
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colorProtein
(map, protList, color)[source]¶ 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’)
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colorRxnType
(map, type, color, width)[source]¶ 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
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colorRxnsFromGenes
(map, model, entrezList, color, areaWidth)[source]¶ 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
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colorSubsystemCD
(map, model, subsystem, color, areaWidth)[source]¶ 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
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compareModelMapFormulas
(model, map, excelName)[source]¶ 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
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correctMetNameCD
(map, metStructure, metList)[source]¶ 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
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correctRxnNameCD
(map, rxnStucture, rxnList)[source]¶ 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
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createColorsMap
()[source]¶ Creates a Map type of structure storing colors by their name in capitals and giving their corresponding HTML color code.
Usage
[colors] = createColorsMap()Output
- 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.
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defaultColorCD
(map)[source]¶ 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
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defaultLookMap
(map)[source]¶ 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
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findMetsFromCompartInMap
(map, compartment)[source]¶ 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
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findMetsInMap
(map, metList)[source]¶ 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
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findRxnsFromCompartInMap
(map, compartment)[source]¶ 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
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findRxnsInMap
(map, rxnList)[source]¶ 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
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findRxnsPerTypeInMap
(map, rxnType)[source]¶ 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)
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getMapMatrices
(map)[source]¶ 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
Create a correspondence of species ID and their index for easier access during the matrix filling
- map –
MATLAB structure of the map
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mapFormula
(map, rxnList)[source]¶ 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
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modifyReactionsMetabolites
(map, rxnList, metList, newColor, newAreaWidth)[source]¶ 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.
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transformFullMap2XML
(xmlStruct, map, fileName)[source]¶ 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.
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transformFullXML2Map
(fileName)[source]¶ 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://opencobra.github.io/cobratoolbox/docs/fullMATLABStructure.html)
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.
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transformMap2XML
(xmlStruct, map, fileName)[source]¶ 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.
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transformToIrreversibleMap
(map, rxnlist)[source]¶ 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
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transformToReversibleMap
(map, rxnlist)[source]¶ 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
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transformXML2Map
(fileName)[source]¶ 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://opencobra.github.io/cobratoolbox/docs/simpleMATLABStructure.html)
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.
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unifyMetabolicMapCD
(map)[source]¶ 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.
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unifyMetabolicPPImapCD
(map)[source]¶ 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