multiple dimensions selectors?

[Noboru Sakabe]

Hi, I'm setting up a track hub and I'm wondering if there is a way
to display multiple "Select subtracy by ..." selectors for data that has
several experimental variables?

I use:

dimensions dimensionX=factor dimensionY=condition

in my composite configuration to display a selector, but I'd like to
have more than one because I have 5 variables that I'd like to be able
to select by.

I tried to declare 2 "dimensions" and only the last one was displayed.

How can I display selectors for multiple variables?

Thanks!

[Brian Lee]

Dear Noboru,

Thank you for using the UCSC Genome Browser and your question about adding multiple dimension selectors in Track Hubs.

You can accomplish this using subGroups and a setting called filterComposite: http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#subGroups

Here is a small example hub using these features and the trackDb.txt:
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://hgwdev.cse.ucsc.edu/~brianlee/hubTesting/hubFilterTest/testDimensions2/hub.txt

This hub's trackDb.txt:
http://hgwdev.cse.ucsc.edu/~brianlee/hubTesting/hubFilterTest/testDimensions2/hg19/trackDb.txt

...
subGroup1 fc Factor a=AAA ...
subGroup2 sc Info s1=100 ...
subGroup3 ts Tissue t1=brain ...
subGroup4 lb Lab l1=UCSC ...
subGroup5 tr Treatment tr1=Alcohol ...
dimensions dimX=fc dimY=ts dimA=sc dimB=lb dimC=tr ...
filterComposite dimA dimB dimC ...
...

A good robust example hub that used many of these more advanced settings that you can explore is the ENCODE Analysis Working Group hub: http:/genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt

If you look into the trackDb.txt of this hub, comparing it to what is visible in the Browser, you will see it is rather large and full of information, but it can give a glimpse of how much you can customize your track hub display in the browser:
http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hg19/trackDb.txt

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute

--

[Noboru Sakabe]

    Thanks, it works great!
    filterComposite does what I want.
    I don't know if it's my browser, but the drop down menu is very small and even with two options I need to scroll it. Just a minor thing.