Added by Mingxun Wang, last edited by Louis Felix Nothias on Sep 07, 2017  (view change)

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Attribute and GROUP Mapping

We strongly recommend to use metadata table instead of group mapping (see above). Group mapping and attribute mapping are supported but should be considered as legacy format.

Using metadata table or 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. 

Examples of Attributes (Source, Subject_ID, Location) and their corresponding GROUPS

  • Source=HUMAN;MOUSE;MICROBE;STOOL;CONTROL
  • Subject_ID=MOUSE1;MOUSE2:MOUSE3;CONTROL
  • Location=California;Arizona;Utah;Colorado;CONTROL

Examples of corresponding GROUPS

  • 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

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. 

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

GROUP_microbe1=1.mzXML;2.mzXML
GROUP_microbe2=3.mzXML;4.mzXML

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 .

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.

Attribute File Format
 attribute1=group1;group2

In the output, a new attribute column will be created with the column header "attribute1" and each entry will be a subset of the groups specific (group1, group2). 

Group Files Format
GROUP_group1=1.mzXML;2.mzXML
GROUP_group2=3.mzXML;4.mzXML

In the output, an attribute called AllGroups will contain a subset of the groups listed above. Note: the prefix GROUP_ must have GROUP be in all caps. 

Caveats

There should be no name collisions between Group names and Attribute names or else the behavior of the output will be undefined.

To create the above files, DO NOT use a word processor of any kind. A text editor MUST be used. If you do not know the difference between the two use Notepad++ on Windows, Text Wrangler on OS X, and gedit on Linux.