Custom BED track itemRgb alpha value

[Chris Cheshire]

Hi there,

I am in the process of creating some custom tracks and I would like to represent score on a coloured element. Currently, I have one greyscale track for strength and another identical track to indicate colour. Ideally I would like to combine the two and have the score fade the alpha value of the colour up and down. Is this possible? I have search the documentation but I cannot see how to do this...

Thanks,

Chris Cheshire (UCL)

[Steve Heitner]

Hello, Chris.

If I understand your question correctly, you are aware of and using the “score” field and “useScore” attribute in your first custom track (as described at http://genome.ucsc.edu/FAQ/FAQformat.html#format1) to color the items in grayscale according to their score.  You are looking to use similar shading, only in colors and not just black/gray, to shade items in light blue to dark blue, light red to dark red, etc.

Assuming this is correct, there is no easy way to accomplish what you’re looking to do.  The best thing I might suggest is to use the itemRgb field for individual items in your bed/bigBed file.  Based on the score of each item, you can assign a specific RGB value for those items.  You would need to determine the specific RGB values for the light-to-dark shades you want to use and then assign them to each item based on that item’s score.  There is an example demonstrating the use of the itemRgb field in the BED format page that I linked above.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  All messages sent to that address are archived on a publicly-accessible Google Groups forum.  If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Steve Heitner
UCSC Genome Bioinformatics Group

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[Chris Cheshire]

Hi Steve,

Thanks for your reply, I thought that might be the case, I wanted to see if there was another option before I went down the color map route! Do you have a feature request list that I this could be added to? I know of a few users who would like this functionality. 

Thanks,

Chris

[Brian Lee]

Dear Chris,

Thank you for using the UCSC Genome Browser and your suggestion to enhance the color display of BED tracks.

Your email will be included in a ticket for this feature and we will notify you when the new code is released, however, at this time, it is not clear when that might happen given existing tasks.

Thank you again for your inquiry and sharing a suggestion to improve 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 togeno...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute

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