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on Jul 24, 2015 17:03.

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Separate documentation is available for both [Molecular Networking Analysis|Molecular Networking Analysis Documentation] and Cytoscape at
[Cytoscape 2.8.X Visualization and Analysis Documentation|Cytoscape 2.8.X Visualization and Analysis Documentation] and [Cytoscape 3.2.X Visualization and Analysis Documentation|Cytoscape 3.2.X Visualization and Analysis Documentation].


!Screenshot 2015-07-22 17.23.12.png|border=1!

h4. Attribute and GROUP Mapping

Alternative to assigning groups when selecting data input files within the workflow of GNPS, a group mapping file and attribute mapping file can be created.  These files allow more flexibility for data analysis and visualization, but requires a specific format. Users must create these file themselves using a text editor (e.g. Notepad+\+ for Windows, gedit for Linux, TextWrangler for Mac OS) and then designating the file extension as .group. *Note:* All .group files can be created, edited, saved and re-opened using a text editor. 

h4. Group Mapping
Attribute and GROUP mapping can greatly ease the visualization and analysis of data within Cytoscape.  The user must group their files using a group mapping file.  The GROUPS are then organized into attribute mapping file. Attributes represent a higher level of organization than GROUPS. A GROUP may be organized into more than one Attribute. 

Alternative to assigning groups when selecting data input files, a group mapping file can be created.  This file allows more flexibility for data analysis, but requires a specific format.
Examples of Attributes (Source, Subject_ID, Location) and their corresponding GROUPS

Users must create this file themselves using a text editor (e.g. Notepad+\+ for Windows, gedit for Linux, TextWrangler for Mac OS). You can download an example in a link below and edit it appropriately. Finally users will need to upload just as you would upload data input files and select it in the Groupings file upload selection. 
* Source=HUMAN;MOUSE;MICROBE;STOOL;CONTROL
* Subject_ID=MOUSE1;MOUSE2:MOUSE3;CONTROL
* Location=California;Arizona;Utah;Colorado;CONTROL

Examples of corresponding GROUPS

Each group in the group mapping must be prefixed with GROUP_. For example:
* GROUP_HUMAN=human1.mzXML;human2.mzXML
* GROUP_MOUSE1=mouse1A.mzXML;mouse1B.mzXML
* GROUP_MOUSE2=mouse2A.mzXML;mouse2B.mzXML
* GROUP_MOUSE=mouse1A.mzXML;mouse1B.mzXML;mouse2A.mzXML;mouse2B.mzXML
* GROUP_California=human2.mzXML;mouse1A.mzXML
* GROUP_CONTROL=Control1.mzXML;Control2.mzXML;Control3.mzXML

GROUP_microbe1=1.mzXML;2.mzXML
GROUP_microbe2=3.mzXML;4.mzXML
Documentation for formatting can be found [here|https://bix-lab.ucsd.edu/display/Public/Molecular+Networking+Group+Attribute+Formats].

h4. Group Mapping

GROUP_microbe1 signifies that the 'microbe1' group contains the files 1.mzXML and 2.mzXML and the 'microbe2' group contains 3.mzXML and 4.mzXML.  Data files can be assigned to more than one group. For a group mapping file template, [click here|^templategrouping.txt].
 You can download an example in a link below and edit it appropriately. Finally users will need to upload just as you would upload data input files and select it in the Groupings file upload selection. 

If you use the group mapping feature, all files can be selected for the G1 group in the basic workflow and the group mapping file is uploaded and selected in the same manner as selecting spectrum files.

Each group in the group mapping must be prefixed with GROUP_. For example:

h4. Attribute Mapping
GROUP_microbe1=1.mzXML;2.mzXML
GROUP_microbe2=3.mzXML;4.mzXML

Attribute mapping eases visualization of different groups within Cytoscape.  First, you group your files in the group mapping file.  A single spectrum can be in multiple groups such as GROUP_organism and GROUP_location.  The groups are then organized into attributes. For example:

location1=microbe1;microbe2
origin2=microbe2
GROUP_microbe1 signifies that the 'microbe1' group contains the files 1.mzXML and 2.mzXML and the 'microbe2' group contains 3.mzXML and 4.mzXML.  Data files can be assigned to more than one group. For a group mapping file template, [click here|^templategrouping.txt].

Groups can be assigned to more than one attribute. In the output, a new attribute column will be created with the column header 'location1' and each entry will be a subset of the groups specific (microbe1, microbe2). For an attribute mapping file template, [click here|^templateattribute.txt].

Documentation for formatting can be found [here|https://bix-lab.ucsd.edu/display/Public/Molecular+Networking+Group+Attribute+Formats].
If you use the group mapping feature, all files can be selected for the G1 group in the basic workflow and the group mapping file is uploaded and selected in the same manner as selecting spectrum files.