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