Tuesday, December 20, 2011

New interface about track selection

New user interface with somewhat radical change has been made for many browser components. I will use examples to introduce all of them.

First one will be heatmap track selection for statistical functions.

Heatmap track selection for pairwise comparison or hypothesis test

The pairwise comparison is to compare two groups of heatmap tracks. Open the pairwise comparison panel you will find two boxes indicating two group holders:

To assign track to group 1, click the "add »" button at top right corner of that box:

A new panel will be displayed with a list of currently displayed heatmap tracks in it. Click on one track name in this panel will assign that track into group 1. Blue background highlights that track as already selected:

Once you're done with the selection click anywhere else on the page to dismiss the track selection panel. Click X signs or buttons to remove track from this group.

The track selection for hypothesis test works in the same way. And don't forget you can do the same thing via right-click menus.

Track selection for correlation analysis

Go to the correlation panel, the interface of which has been stripped down to two buttons as the only operable components (compared with the cluttering old interface):

Click the first button, the heatmap selection panel will appear to let you select a track and run correlation against it:

Once a heatmap track has been selected, the panel will disappear and the correlation is turned on for that:

You can also choose a genomic feature track for correlation. Click that button for it:

This is a list of curated human genomic feature tracks available on the browser. As described before, genomic feature tracks are in separate groups and are arranged in parent-child style. In this panel, the left column is group names (Genes, Repeats, ...) and right is the collection of tracks belonging to this group. The arrow indicates there are children tracks associated with that track, and click it to reveal that:

So back to the correlation function, clicking on one of the genomic feature tracks will invoke correlation with that track (if the track is positional data like genes, correlation will be performed with its density data).

And as always, you can select a track for correlation via right-click menu options.

Managing genomic feature tracks

So here comes what I believe to be the most dramatic change: genomic feature track management component. Go to that panel:

A box is in the panel containing so called "your collection of genomic feature tracks". The browser provides many tracks but you might only be interested in a limited number of them. Having them neatly listed in this place would make management much easier compared with the old way.

Each entry in the list gently presents essential information about the track: name, type (bigBed), mode selector, removal button. Use the drop-down menu to change display mode:

And click the "Add more »" button opens the genomic feature track selection panel you've seen. You just take a look at the inventory, click on a track and it will be added to your list:

Other functions involving the use of track selection panel

1. Genomic juxtaposition

Selecting a track in this way will launch genomic juxtaposition for this track.

1. you can only select genomic feature tracks with positional data, like genes, CpG islands, ... but not those with quantitative data, like GC content or conservation score.
2. Be aware about the amount of features displayed. If there's too many features displayed, running juxtaposition might take quite a bit of time (also depends on number of tracks are there in genome heatmap).

2. Gene Set sorting by track score

This option can be found after you run the Gene Set View. By choosing a heatmap track you can sort genes by their average score over that track.

Gene Plot

You will see this in the Gene Plot panel, where you will determine which quantitative track to be used for Gene Plot. You can either select any of the heatmap tracks, or select a genomic feature track with quantitative data (not the ones like gene model tracks).


So now you might discover that buttons with » indicates it would launch a selector panel when pressed. Trust me I will stick to that.

These small revisions simplified the user interface of each function talked above, and made them consistent with each other, and got code complexity reduced. We hope you agree and would like to hear how you think.