diff --git a/tutorials/visualization/metabolicCartography/tutorial_metabolicCartography.m b/tutorials/visualization/metabolicCartography/tutorial_metabolicCartography.m index 83d6e1b8fc..591f713e3c 100644 --- a/tutorials/visualization/metabolicCartography/tutorial_metabolicCartography.m +++ b/tutorials/visualization/metabolicCartography/tutorial_metabolicCartography.m @@ -446,35 +446,37 @@ %% *2. Research of indexes in the map structure* % Basic functions were created to simplify the manipulation of maps. % -% The function |findRxnsPerType| gives a list of desired reactions based +% The function |findRxnsPerTypeInMap| gives a list of desired reactions based % on the reaction type (2nd colum), and the index for those reactions in |map.rxnName| % (1st colum). %% -transportReactionsIndexList = findRxnsPerType(mapGlyCorrected, 'TRANSPORT'); +transportReactionsIndexList = findRxnsPerTypeInMap(mapGlyCorrected, 'TRANSPORT'); %% -% The function |findMetsIDs| finds the IDs of specific metabolites in |map.specName| -% given a list of metabolites. +% The function |findMetsInMap| finds the IDs of specific metabolites in +% |map.specName| given a list of metabolites. -ATPADPIndexList = findMetsIDs(mapGlyCorrected, ... +ATPADPIndexList = findMetsInMap(mapGlyCorrected, ... {'atp[c]', 'adp[c]', 'atp[m]', 'adp[m]'}); %% -% The function |findRxnsIDs| finds the IDs of specific reactions in |map.rxnName| +% The function |findRxnsInMap| finds the IDs of specific reactions in |map.rxnName| % given a list of reactions. -rxnOfInterestIndexList = findRxnsIDs(mapGlyCorrected, ... +rxnOfInterestIndexList = findRxnsInMap(mapGlyCorrected, ... {'FBP', 'FBA', 'GAPD', 'PFK', 'ENO'}); %% -% The function |findMetFromCompartMap| finds all metabolites in the map +% The function |findMetsFromCompartInMap| finds all metabolites in the map % associated to a specific compartment by looking at the composition of metabolite % names (example: mitochondrial atp = atp*[m]*). [mitochondrialMetsNameList,mitochondrialMetsIndexList] = ... - findMetFromCompartMap(mapGlyCorrected, '[m]'); + findMetsFromCompartInMap(mapGlyCorrected, '[m]'); %% -% The function |findRxnFromCompartMap| finds all reactions in the map associated -% to a specific compartment by looking at the composition of metabolite names. +% The function |findRxnsFromCompartInMap| finds all reactions in the map +% associated to a specific compartment by looking at the composition of metabolite +% names. -mitochondrialRxnsIndexList = findRxnFromCompartMap(mapGlyCorrected, '[m]'); +mitochondrialRxnsIndexList = ... + findRxnsFromCompartInMap(mapGlyCorrected, '[m]'); %% Visualisation of Metabolic and PPI networks % Some of the aforementioned functions were addapted to be used in metabolic % and PPi maps. Some examples are shown below: diff --git a/tutorials/visualization/metabolicCartography/tutorial_metabolicCartography.mlx b/tutorials/visualization/metabolicCartography/tutorial_metabolicCartography.mlx index eaaaf13563..4af22a219f 100644 Binary files a/tutorials/visualization/metabolicCartography/tutorial_metabolicCartography.mlx and b/tutorials/visualization/metabolicCartography/tutorial_metabolicCartography.mlx differ