Monday, September 23, 2013

v24 (3 of 3): facet panel

"Facet panel" is a meaningful way to present large track set using metadata annotation. Version 24 features much improved facet table function.
  • Improved user interface design
  • Unified support on both native and custom metadata vocabularies


  Find the facet panel  
At the browser, click "Tracks" > "Experimental assay tracks". Following panel will be shown (example from hg19):



To change row definitions (principle facets), click "Sample" on the header to see available choices:


The facet panel can be configured into a tree by using only the Row option:




  Facet panel for custom metadata  

First, load a datahub. You can click following link to load a public hub in hg18 genome:

http://epigenomegateway.wustl.edu/browser/?genome=hg18&publichub=mm1s

Then open the facet panel:


Now you can see two facet tables. The table on top in colored border is from the public hub (named Multiple Myeloma Data Gateway).  The table on the bottom is the original native metadata vocabulary. The two tables are organized by two separate metadata vocabularies, but can be used in the same way.



  Using metadata colormap  

Both native and custom metadata terms can be chosen for display in metadata color map. Right click on the terms and choose "Add" option:


The metadata vocabulary tree will be shown. Check the checkbox for a term to add this term to color map. If a custom vocabulary has been loaded, it will also be shown as a tree with shaded background, along with the native tree: