forked from opencobra/cobratoolbox
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request opencobra#1057 from opencobra/develop
Regular merge of develop
- Loading branch information
Showing
1,195 changed files
with
482,450 additions
and
74,889 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| .. _metabolicCartography: | ||
|
|
||
| MetabolicCartography | ||
| -------------------- | ||
|
|
||
| .. automodule:: src.visualization.metabolicCartography | ||
| :members: |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -10,6 +10,7 @@ Visualization | |
|
|
||
| cellDesigner | ||
| maps | ||
| metabolicCartography | ||
|
|
||
| .. automodule:: src.visualization | ||
| :members: | ||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,107 @@ | ||
| # Output description of the function `transformFullXML2Map` | ||
|
|
||
| ### Specifics | ||
|
|
||
| To be able to modify maps containg Protein-Protein Interactions (PPI) | ||
| created in CellDesigner from MATLAB, they have to be first parsed using the | ||
| function "transformFullXML2Map". Compared to a simple Metabolic map, PPI maps | ||
| contain Proteins and Complexes and must therefore be stored accordingly. | ||
| When manipulating Metabolic only maps, please refer to the | ||
| [`transformXML2Map` function's output description](simpleMATLABStructure.md). | ||
|
|
||
| ### Content | ||
|
|
||
| This function will extract the relevant annotations from the XML file | ||
| and create a particular structure containg these annotations, that would | ||
| be later modified using various functions from the COBRA Toolbox. | ||
| Using this function, the MATLAB structure contains the following fields: | ||
|
|
||
| 1. Molecules information (specific to each node in the map) | ||
| 2. Complexes information (specific to each entity in the map) | ||
| 3. Included Species information (specific to each entity in the map) | ||
| 4. Species information (specific to each entity in the map) | ||
| 5. Reactions information (with their corresponding modifications) | ||
| 6. Compartment information (if existing in the map) | ||
| 7. Matrices (specific for the map and comparable with the model) | ||
|
|
||
|
|
||
| | **Field name** | **Dimension** | **Data Type** | **Field description** | | ||
| |:---:|:---:|:---:|:---:| | ||
| | **Molecules information** | | ||
| | `map.molAlias` | `a x 1` | cell of char | Alias of each molecules (no duplicates) | | ||
| | `map.molID` | `a x 1` | cell of char | ID of each molecules (duplicates) | | ||
| | `map.molCompartAlias` | `a x 1` | cell of char | Corresponding compartment alias of each molecules (EMPTY if no info) | | ||
| | `map.molXPos` | `a x 1` | cell of char or double | X position of each molecules (stored as string but can be changed to double) | | ||
| | `map.molYPos` | `a x 1` | cell of char or double | Y position of each molecules (stored as string but can be changed to double) | | ||
| | `map.molWidth` | `a x 1` | cell of char or double | Width of each molecules (stored as string but can be changed to double) | | ||
| | `map.molHeight` | `a x 1` | cell of char or double | Height of each molecules (stored as string but can be changed to double) | | ||
| | `map.molColor` | `a x 1` | cell of char | Color of each molecules (in "HTML" code with lowercases and "ff" instead of "#' at the beginning) | | ||
| | **Complexes information** | | ||
| | `map.complexAlias` | `c x 1` | cell of char | Alias of each complex (no duplicates) | | ||
| | `map.complexID` | `c x 1` | cell of char | ID of each complex (duplicates) | | ||
| | `map.complexCompartAlias` | `c x 1` | cell of char | Corresponding compartment alias of each complex (EMPTY if no info) | | ||
| | `map.complexXPos` | `c x 1` | cell of char or double | X position of each complex (stored as string but can be changed to double) | | ||
| | `map.complexYPos` | `c x 1` | cell of char or double | Y position of each complex (stored as string but can be changed to double) | | ||
| | `map.complexWidth` | `c x 1` | cell of char or double | Width of each complex (stored as string but can be changed to double) | | ||
| | `map.complexHeight` | `c x 1` | cell of char or double | Height of each complex (stored as string but can be changed to double) | | ||
| | `map.complexColor` | `c x 1` | cell of char | Color of each complex (in "HTML" code with lowercases and "ff" instead of "#' at the beginning) | | ||
| | **Included Species information** | | ||
| | `map.specIncID` | `i x 1` | cell of char | ID of each included species (no duplicates) | | ||
| | `map.specIncProtID` | `i x 1` | cell of char | Protein ID reference of each included species | | ||
| | `map.specIncCplxID` | `i x 1` | cell of char | Complex ID reference of each included species | | ||
| | `map.specIncName` | `i x 1` | cell of char | Name of each included species | | ||
| | `map.specIncType` | `i x 1` | cell of char | Type of each species (SIMPLE_MOLECULE/ION/PROTEIN...) | | ||
| | `map.specIncNotes` | `i x 1` | cell of char | Notes of each included species (EMPTY if no info) | | ||
| | **Species information** | | ||
| | `map.specID` | `s x 1` | cell of char | ID of each species (no duplicates) | | ||
| | `map.specMetaID` | `s x 1` | cell of char | MetaID of each species often related to ID (no ducplicates) | | ||
| | `map.specName` | `s x 1` | cell of char | Name of each species | | ||
| | `map.specType` | `s x 1` | cell of char | Type of each species (SIMPLE_MOLECULE/ION/PROTEIN...) | | ||
| | `map.specNotes` | `s x 1` | cell of char | Notes of each species (EMPTY if no info) | | ||
| | **Reactions information** | | ||
| | `map.rxnID` | `r x 1` | cell of char | ID of each reactions (no duplicates) | | ||
| | `map.rxnMetaID` | `r x 1` | cell of char | MetaID of each reactions | | ||
| | `map.rxnName` | `r x 1` | cell of char | Name of each reactions | | ||
| | `map.rxnType` | `r x 1` | cell of char | Type of each reactions | | ||
| | `map.rxnReversibility` | `r x 1` | cell of char | Reversibility of each reactions (false or true) | | ||
| | `map.rxnBaseReactantAlias` | `r x p x 1` | cell of cell of char | Alias of the base reactant(s) | | ||
| | `map.rxnBaseReactantID` | `r x p x 1` | cell of cell of char | ID of the base reactant(s) | | ||
| | `map.rxnBaseProductAlias` | `r x p x 1` | cell of cell of char | Alias of the base product(s) | | ||
| | `map.rxnBaseProductID` | `r x p x 1` | cell of cell of char | ID of the base product(s) | | ||
| | `map.rxnReactantAlias` | `r x p x 1` | cell of cell of char | Alias of reactant(s) (EMPTY if not present) | | ||
| | `map.rxnReactantID` | `r x p x 1` | cell of cell of char | ID of reactant(s) (EMPTY if not present) | | ||
| | `map.rxnReactantLineType` | `r x p x 1` | cell of cell of char | Type of the reactant's reaction line ('Curve' or 'Straight') | | ||
| | `map.rxnReactantLineColor` | `r x p x 1` | cell of cell of char | Color of the reactant's reaction line (in "HTML" code with lowercases and "ff" instead of "#' at the beginning) | | ||
| | `map.rxnReactantLineWidth` | `r x p x 1` | cell of cell of char or double | Width of the reactant's reaction line | | ||
| | `map.rxnProductAlias` | `r x p x 1` | cell of cell of char | Alias of product(s) (EMPTY if not present) | | ||
| | `map.rxnProductID` | `r x p x 1` | cell of cell of char | ID of product(s) (EMPTY if not present) | | ||
| | `map.rxnProductLineType` | `r x p x 1` | cell of cell of char | Type of the product's reaction line ('Curve' or 'Straight') | | ||
| | `map.rxnProductLineColor` | `r x p x 1` | cell of cell of char | Color of the product's reaction line (in "HTML" code with lowercases and "ff" instead of "#' at the beginning) | | ||
| | `map.rxnProductLineWidth` | `r x p x 1` | cell of cell of char or double | Width of the product's reaction line | | ||
| | `map.rxnModAlias` | `r x p x 1` | cell of cell of char | Alias of modifiers metabolites of each reactions | | ||
| | `map.rxnModID` | `r x p x 1` | cell of cell of char | ID of modifiers metabolites of each reactions | | ||
| | `map.rxnModType` | `r x p x 1` | cell of cell of char | Type of the modification by the metabolite of each reactions | | ||
| | `map.rxnModColor` | `r x p x 1` | cell of cell of char | Color of the modification line of each reactions | | ||
| | `map.rxnModWidth` | `r x p x 1` | cell of cell of char or double | Width of the modification line of each reactions | | ||
| | `map.rxnColor` | `r x 1` | cell of char | Color of the main reaction (in "HTML" code with lowercases and "ff" instead of "#' at the beginning) => later modified for the whole reaction's members | | ||
| | `map.rxnWidth` | `r x 1` | cell of char | Width of the main reaction (stored as string but can be changed to double) => later modified for the whole reaction's members | | ||
| | `map.rxnNotes` | `r x 1` | cell of char | Notes of each reactions (EMPTY if no info) | | ||
| | **Compartment information** | | ||
| | `map.compartAlias` | `c x 1` | cell of char | Alias of each compartments (EMPTY if no info) | | ||
| | `map.compartName` | `c x 1` | cell of char | Name of each compartments (EMPTY if no info) | | ||
| | **Matrices** | | ||
| | `map.sID` | `s x r` | logical | Logical matrix with rows = speciesID and columns = reactionsID | | ||
| | `map.sAlias` | `m x r` | logical | Logical matrix with rows = speciesAlias and columns = reactionsID | | ||
| | `map.idAlias` | `s x m` | logical | Logical matrix widh rows = speciesID and columns = speciesAlias | | ||
|
|
||
|
|
||
| ### Note: | ||
|
|
||
| The dimension `p` is variable between reactions as each reaction can contain one | ||
| or more Base Reactants or Products and the same is possible for Reactants, | ||
| Products and Modifiers. Therefore, this value is not static and varies in all | ||
| reactions. | ||
|
|
||
| Please note also that logical matrices are disabled for the moment for PPI maps. | ||
| To be structured as the model and to be comparable, the access to entities has | ||
| to be adapted for such maps as the models do not contain Proteins at the moment. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| # Output description of the function `transformXML2Map` | ||
|
|
||
| ### Specifics | ||
|
|
||
| To be able to modify metabolic maps created in CellDesigner from MATLAB, | ||
| they have to be first parsed using the function "transformXML2Map". | ||
| A metabolic map contains only Simple molecules, such as Ions, Metabolites... | ||
| When manipulating maps with Protein-Protein Interactions, please refer to the | ||
| [`transformXML2Map` function's output description](fullMATLABStructure.md). | ||
|
|
||
| ### Content | ||
|
|
||
| This function will extract the relevant annotations from the XML file | ||
| and create a particular structure containg these annotations, that would | ||
| be later modified using various functions from the COBRA Toolbox. | ||
| Using this function, the MATLAB structure contains the following fields: | ||
|
|
||
| 1. Molecules information (specific to each node in the map) | ||
| 2. Species information (specific to each entity in the map) | ||
| 3. Reactions information (with their corresponding modifications) | ||
| 4. Compartment information (if existing in the map) | ||
| 5. Matrices (specific for the map and comparable with the model) | ||
|
|
||
|
|
||
| | **Field name** | **Dimension** | **Data Type** | **Field description** | | ||
| |:---:|:---:|:---:|:---:| | ||
| | **Molecules information** | | ||
| | `map.molAlias` | `a x 1` | cell of char | Alias of each molecules (no duplicates) | | ||
| | `map.molID` | `a x 1` | cell of char | ID of each molecules (duplicates) | | ||
| | `map.molCompartAlias` | `a x 1` | cell of char | Corresponding compartment alias of each molecules (EMPTY if no info) | | ||
| | `map.molXPos` | `a x 1` | cell of char or double | X position of each molecules (stored as string but can be changed to double) | | ||
| | `map.molYPos` | `a x 1` | cell of char or double | Y position of each molecules (stored as string but can be changed to double) | | ||
| | `map.molWidth` | `a x 1` | cell of char or double | Width of each molecules (stored as string but can be changed to double) | | ||
| | `map.molHeight` | `a x 1` | cell of char or double | Height of each molecules (stored as string but can be changed to double) | | ||
| | `map.molColor` | `a x 1` | cell of char | Color of each molecules (in "HTML" code with lowercases and "ff" instead of "#' at the beginning) | | ||
| | **Species information** | | ||
| | `map.specID` | `s x 1` | cell of char | ID of each species (no duplicates) | | ||
| | `map.specMetaID` | `s x 1` | cell of char | MetaID of each species often related to ID (no ducplicates) | | ||
| | `map.specName` | `s x 1` | cell of char | Name of each species | | ||
| | `map.specType` | `s x 1` | cell of char | Type of each species (SIMPLE_MOLECULE/ION/PROTEIN...) | | ||
| | `map.specNotes` | `s x 1` | cell of char | Notes of each species (EMPTY if no info) | | ||
| | **Reactions information** | | ||
| | `map.rxnID` | `r x 1` | cell of char | ID of each reactions (no duplicates) | | ||
| | `map.rxnMetaID` | `r x 1` | cell of char | MetaID of each reactions | | ||
| | `map.rxnName` | `r x 1` | cell of char | Name of each reactions | | ||
| | `map.rxnType` | `r x 1` | cell of char | Type of each reactions | | ||
| | `map.rxnReversibility` | `r x 1` | cell of char | Reversibility of each reactions (false or true) | | ||
| | `map.rxnBaseReactantAlias` | `r x p x 1` | cell of cell of char | Alias of the base reactant(s) | | ||
| | `map.rxnBaseReactantID` | `r x p x 1` | cell of cell of char | ID of the base reactant(s) | | ||
| | `map.rxnBaseProductAlias` | `r x p x 1` | cell of cell of char | Alias of the base product(s) | | ||
| | `map.rxnBaseProductID` | `r x p x 1` | cell of cell of char | ID of the base product(s) | | ||
| | `map.rxnReactantAlias` | `r x p x 1` | cell of cell of char | Alias of reactant(s) (EMPTY if not present) | | ||
| | `map.rxnReactantID` | `r x p x 1` | cell of cell of char | ID of reactant(s) (EMPTY if not present) | | ||
| | `map.rxnReactantLineType` | `r x p x 1` | cell of cell of char | Type of the reactant's reaction line ('Curve' or 'Straight') | | ||
| | `map.rxnReactantLineColor` | `r x p x 1` | cell of cell of char | Color of the reactant's reaction line (in "HTML" code with lowercases and "ff" instead of "#' at the beginning) | | ||
| | `map.rxnReactantLineWidth` | `r x p x 1` | cell of cell of char or double | Width of the reactant's reaction line | | ||
| | `map.rxnProductAlias` | `r x p x 1` | cell of cell of char | Alias of product(s) (EMPTY if not present) | | ||
| | `map.rxnProductID` | `r x p x 1` | cell of cell of char | ID of product(s) (EMPTY if not present) | | ||
| | `map.rxnProductLineType` | `r x p x 1` | cell of cell of char | Type of the product's reaction line ('Curve' or 'Straight') | | ||
| | `map.rxnProductLineColor` | `r x p x 1` | cell of cell of char | Color of the product's reaction line (in "HTML" code with lowercases and "ff" instead of "#' at the beginning) | | ||
| | `map.rxnProductLineWidth` | `r x p x 1` | cell of cell of char or double | Width of the product's reaction line | | ||
| | `map.rxnModAlias` | `r x p x 1` | cell of cell of char | Alias of modifiers metabolites of each reactions | | ||
| | `map.rxnModID` | `r x p x 1` | cell of cell of char | ID of modifiers metabolites of each reactions | | ||
| | `map.rxnModType` | `r x p x 1` | cell of cell of char | Type of the modification by the metabolite of each reactions | | ||
| | `map.rxnModColor` | `r x p x 1` | cell of cell of char | Color of the modification line of each reactions | | ||
| | `map.rxnModWidth` | `r x p x 1` | cell of cell of char or double | Width of the modification line of each reactions | | ||
| | `map.rxnColor` | `r x 1` | cell of char | Color of the main reaction (in "HTML" code with lowercases and "ff" instead of "#' at the beginning) => later modified for the whole reaction's members | | ||
| | `map.rxnWidth` | `r x 1` | cell of char | Width of the main reaction (stored as string but can be changed to double) => later modified for the whole reaction's members | | ||
| | `map.rxnNotes` | `r x 1` | cell of char | Notes of each reactions (EMPTY if no info) | | ||
| | **Compartment information** | | ||
| | `map.compartAlias` | `c x 1` | cell of char | Alias of each compartments (EMPTY if no info) | | ||
| | `map.compartName` | `c x 1` | cell of char | Name of each compartments (EMPTY if no info) | | ||
| | **Matrices** | | ||
| | `map.sID` | `s x r` | logical | Logical matrix with rows = speciesID and columns = reactionsID | | ||
| | `map.sAlias` | `m x r` | logical | Logical matrix with rows = speciesAlias and columns = reactionsID | | ||
| | `map.idAlias` | `s x m` | logical | Logical matrix widh rows = speciesID and columns = speciesAlias | | ||
|
|
||
| *** Note: | ||
|
|
||
| The dimension `p` is variable between reactions as each reaction can contain one | ||
| or more Base Reactants or Products and the same is possible for Reactants, | ||
| Products and Modifiers. Therefore, this value is not static and varies in all | ||
| reactions. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.