ReconMaps¶
- buildFluxDistLayout(minerva, model, solution, identifier, hexColour, maxThickness, content)¶
Builds a layout for MINERVA from a flux distribution. If a dictionary of identifiers is not provided it is assumed that the map and the COBRA model’s nomenclature is coherent. Sends the layout to the remote MINERVA instance
USAGE:
[serverResponse] = buildFluxDistLayout( minerva, model, solution, identifier, hexColour, thickness, content)
- INPUTS:
- minerva: Struct with the information of minerva instance:
address, login, password and model (map)
model: COBRA model structure solution.v: optimizeCb solution structure with a flux vector identifier: Name for the layout in MINERVA
- OPTIONAL INPUT:
- hexColour colour of overlay (hex color format)
e.g. ‘#009933’ corresponds to http://www.color-hex.com/color/009933 If you want to make a color gradient, you can input an array of 2 or 3 colors like [“#ff0000”, “#6617B5”, “#0000ff”] note that they should be declared with (”) rather than with (‘)
maxThickness: maximum thickness content: character array with the following format for each
reaction to be displayed. Bypasses the use of solution.v to set the format. ‘name%09reactionIdentifier%09lineWidth%09color%0D’
- OUTPUT:
serverResponse: Response of the MINERVA
- changeCbMapOutput(outputFormat)¶
changeCbMapOutput sets the output format for drawCbMap. Displays outputFormat if no inputs provided.
outputFormatOK = changeCbMapOutput(outputFormat)
- OPTIONAL INPUT
- outputFormat drawCbMap render format
{‘svg’, ‘matlab’, ‘java’} (java not implemented)
- OUTPUT
outputFormatOK True if output format set properly, else false.
- generateSubsystemLayouts(minerva, cobra_model, color)¶
Generates subsystem layouts
USAGE:
generateSubsystemLayouts( minerva, cobra_model, color )
- INPUTS:
- minerva: Struct with the information of minerva instance:
address, login, password and model (map)
cobra_model: COBRA model structure color: Color
- generateSubsytemsLayout(minerva, cobra_model, subsystem, color)¶
Generates subsystem layouts
USAGE:
generateSubsytemsLayout(minerva, cobra_model, subsystem, color)
- INPUTS:
- minerva: Struct with the information of minerva instance:
address, login, password and model (map)
cobra_model: COBRA model structure subsystem: Subsystem color: Color
- makeColorGradient(col1, col2, ncol)¶
Generates a color gradient in hex format, based on color 1 and 2
USAGE:
[cmap] = makeColorGradient(col1, col2, ncol)
- INPUTS:
col1: First color col2: Last color ncol: Number of colors in between
- OUTPUT:
- cmap: Color gradient map with the corresponding
colors in hex format
- postMINERVArequest(login, password, map, googleLicenseContent, identifier, content)¶
Sends a new layout to a MINERVA instance
USAGE:
[response] = postMINERVArequest(minerva_servlet, login, password, map, identifier, content)
- INPUTS:
minerva_servlet: URL login: MINERVA username password: MINERVA password map: MINERVA map googleLicenseContent: True if user agreed to Google Maps terms of
identifier: Layout name content: Content of the layout
- OUTPUT:
- response: MINERVA’s response - cell array index 1 - 0/1
whether the overlay was successfully uploaded. index 2 - success or error message
- printInRecon3Dmap(rxnList, colorValues, outputDir, lineWidth, fileName)¶
This function generates a TXT file that can be integrated in the VMH database (vmh.life) to overlay certain reactions
USAGE:
printInRecon3Dmap(rxnList, output, values)
- INPUTS:
rxnList: List of rxn to be higligted colorValues: Numerical value for each reaction (to assign
different colors (default: 0
- outputDir: Directory where the file will be created
(default: current directory)
lineWidth: Numerical value of line width to set. default=8 fileName: File name prefix for the output file. Should be a char array.
default is ‘C__fakepath_data4ReconMap3_’.
OUTPUTS
Text file used as an input for the VMH database