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dasmoth / dalliance

Interactive web-based genome browser.
http://www.biodalliance.org/
BSD 2-Clause "Simplified" License
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Visualising boundary cases for peak calls #37

Open jurgjn opened 11 years ago

jurgjn commented 11 years ago

Peak calling (as well as several other bioinformatics analyses) often involves selecting a threshold of some kind (e.g. FDR, p-value, peak area). It would be useful to have a UI for quickly finding and browsing through a set of regions that contain peaks around a specified threshold value to develop an visual intuition for the resulting FP/FN cases.

dasmoth commented 11 years ago

Browsing bigWig tracks "by threshold" has been supported since Dalliance 0.9, although it is still undergoing a bit of development work.

If adding a track using the Dalliance API, this can be enabled by specifying:

      quantLeapThreshold:  42,

...which enables quantitative leap mode and sets the default threshold to 42. If setting up a trackhub-style configuration file, use:

     yLineOnOff on
     yLineMark 42

Configuring quantitative leaping for tracks added via the manual UI is currently work in progress.

When it's enabled, you will see the threshold shown as a red line. Select a tier (click on its label track until it is highlighted with a blue outline). Then adjust the threshold using CTRL + up/down arrows, and leap to the next region over the threshold using CTRL + left/right arrows.