Extending Embedding and Customizing JBrowse
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
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