Tuesday, January 17, 2012

Minor improvement to Gene Plot

The Gene Plot function has previously been designed to work primarily downstream of Gene Set View. It takes genomic coordinates used in Gene Set View to do the plot. It also has been extended to work with custom bigBed track, where all coordinates of bigBed track can be used in Gene Plot.

Now Gene Plot can be run like a standalone App, so that you can easily make a plot using list of genes or coordinates. Launch it by clicking button  in floating toolbox and select the option:


The Gene Plot panel will now be displayed as a floating panel on top of Browser page (partially shown):


In addition to old steps 1-2-3, "Step 0" is added here, where you can specify positional data for the plot. Its usage is entirely same as Gene Set View interface.

Once positional data is specified, continue with remaining steps by choosing data track (step 2), choosing plot type (step 3), and rendering mechanism (step 4). Push button to run Gene Plot. After a short while the plot will be displayed in a new panel.