Thursday, September 15, 2011

Gene Plot for custom bigBed track

So now the Gene Plot can be applied to a custom bigBed track, where features inside that track will be used to query data and organize the plot. Let's start by uploading a custom bigBed file.


At navigation bar, go to Tracks > Custom track > bigBed, ready to submit the sample bigBed file:


Click submit, the track will be up there:


This sample track actually contains gene body information, as you can tell by comparing with "gene body" track.

There's a orange-colored button in the custom track table entry. Click it to launch Gene Plot panel. Alternatively, you can right click on the bigBed track image, choose "Gene Plot" option to get that:


Once launched, the Gene Plot panel will pop out from thin air:



Here you see the familiar Step 1,2,3 to make gene plot. But pay attention to the little message above Step 1. It complains that this bigBed track contains too many items that it will only process the first 4000. Well, the intent of applying Gene Plot on a bigBed track is to use ALL items it contains, but before we get powerful enough servers I don't want that to crash the browser service... So please abide this restriction for this current moment. And anyway, this is already a big increase compared with Gene Set View (<300 items).


Choose your favorite graph type and make the plot. The figure will show up in another panel on the top. Once you're done looking at it, click the button at top-right corner to dismiss the panels.

So this is the way to use it. If you have long list of target genes, you can use the bigBed generator to make the file, have it up on browser and run Gene Plot on it. I think it's cool, and hope you'll enjoy it.

However pitfall lurks here. The second plot type, the "spaghetti plot", can be dangerous if applied with Google Chart service with large item number. It will use so much client-side memory that might hang your little laptop (I've done that on my desktop with 8gb RAM). As a primary way of protection, this plot will reject attempts with over 500 items. However you can use R as rendering method to bypass this restriction.




All the same stuff apply to Gene Set View. Following is a quick survey:


Click large orange button to launch Gene Plot on this gene set:


Make a plot:



So that's it. By looking at the stack of platters in above screen shot, you might recognized this is a new style in my browser. I might be using such style more repeatedly in future. Let me know how you think.