Minor extension to Bird's Eye View

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Tuesday, January 17, 2012

Following previous post, select and launch Bird's Eye View via option from floating toolbox:

Minor extension to Bird's Eye View 1 1.png

The Bird's Eye View interface panel will be displayed on top of page:

Minor extension to Bird's Eye View 2 1.png

In the beginning, no data is been displayed in the View Panel, and this is indicated by "No data on show" on top of panel.

At this step you can add and display tracks in the View Panel. To add a heatmap track, press first button:

Minor extension to Bird's Eye View 3 2.png

The heatmap track selection panel appears prompting you to make selection. Select one and it will be displayed in the view:

Minor extension to Bird's Eye View 4 3.png

Once some data has been displayed, a button Show list of data will be displayed instead. Push it to show the list of tracks available in the View Panel:

Minor extension to Bird's Eye View 5 4.png

Finally, you might be wondering where is the large wrench button. It has been moved into the View Panel, on the header line. Click it to show the configuration panel in floating toolbox:

Minor extension to Bird's Eye View 6 5.png

As indicated, you can configure appearance of View Panel using the options here.


Still substantial amount of work need to be done to make this function better. First of all, as Genome-wide statistics and visual display statistical tracks can run in the framework of Bird's Eye View], however they don't work with chromosome resizing, that's what the option "Width of longest chromosome" does. Right now when you resize chromosomes, statistical tracks will be removed to avoid error. This is certainly inconvenient, but as a complete code revision is required to make this desirable feature possible, this takes a bit of time, and I beg your pardon on this.

The other more fun and challenging stuff is to support metabolic pathway in Bird's Eye View. The words on top left corner "Display data on whole genome" reserves place for this function. In the future an option looking like something below will be deployed here:

Display data on whole genomeKEGG pathwaysBioCyc pathwaysBioCarta pathways

By this you can switch view by one mouse click and view profile of your data on hundreds of pathways, how exciting that would be! But first I need to sort out some technical details like whether to host local copy of pathway database or do real-time query, and whether to use plain row display or network charts.