Extending Embedding and Customizing JBrowse

From GMOD
Jump to: navigation, search

Result of discussions at GMOD satellite meeting, March 2011

Potential upcoming changes to JSON format:

http://biowiki.org/view/JBrowse/JsonFormatStabilization

TODO/wishlist for JBrowse:

  • namespace CSS
  • putting track list into separate DOM element (e.g., Drupal "block")
  • "Browser" API: anything you can do manually
  • Hooks:
    • featureCreate: has access to: feature data, feature HTML element, can:
      • style the element, and
      • add callbacks to the element
    • featureEventHooks:
{ click: function(feature array, HTML element, getAttr, event)
 mouseover: function(...
 mouseout: ...
 [DOM event name]: [callback function]
}
current approach:
fields:
{ "start": 1,
  "end": 2,
  "strand": 3,
  ...
}
changing to: getAttr
    • access to region selections (e.g., for creation of lists of features)
    • function that: takes currently visible sequence, PSSM or set of regexes, returns: set of regions

"Browser" API extensions:

Browser.iterateFeaturesInTrack("gene", function(feature, elem, getAttr) {if (getAttr(feature, "id") == "foo") {elem.style.backgroundColor="red"}})

?Browser.filterTrackBy("gene", function(feature, elem, getAttr { return (getAttr(feature, "id") == "foo") });

e.g.,

  • all genes in a given pathway with expression > 2 s.d. above average
  • all genes tagged with a given GO term

sequence logos for summarizing overlapping alignments

common GBrowse glyphs not currently reproducible in JBrowse:

  • LD plot? (not common)
  • GBrowse uses gene->mRNA relationships to layout ("bump") transcripts for a given gene together.
  • GBrowse shows different representation of break between read pairs and gaps within individual reads
  • Glyph/image.pm (associates images with seqfeatures)


General JBrowse feature requests:

  • "no data" screen a la GBrowse
  • example data to browse included distribution
  • region selection