Hello Malcolm, Using a BED file with each item defined with a color value would work. Then, set the display to "dense" to collapse the view.
To see how this works, use the example I sent earlier at the end of this BED custom track description. http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 3/23/10 10:07 AM, Cook, Malcolm wrote: > Jennifer, > > I am interested in the colorByStrand option to BedGraph format mentioned > below. > > Are there any other developments along these lines (i.e. track coloring > options) that you can share with us....??? > > In particular, I would greatly benefit from being able to use color to > differentiate sub-regions within a BED12-specified region, in a similar way > as being able to have THICK and not thick regions. > > Barring that, I wonder if there is a way to compose a single graphical "item" > out of multiple annotation lines, one for each segment. I believe that using > GFF I could group multiple lines using column 9, each line having a different > "score" resulting in a single "item" with different segments each having its > own "level of gray". I am searching for something similar, except (1) with > color and (2) possibly BED (and > > > Thanks! > > Malcolm Cook > Stowers Institute for Medical Research - Bioinformatics > Kansas City, Missouri USA > > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Jennifer Jackson > Sent: Monday, March 22, 2010 1:55 PM > To: Tien-chi Pan > Cc: [email protected] > Subject: Re: [Genome] BedGraph label color > > Hi Tien-chi, > > You are correct, there are limits in the color options for bedGraph. The > other formats are necessary for the display you explained. > > Thanks, > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 3/21/10 7:06 PM, Tien-chi Pan wrote: >> Hi Jennifer, >> >> Thanks for the suggestions. I failed to mention that I would like to >> display bars with varying heights proportional to my input continuous >> variable (the main reason why I picked bedGraph). My understanding is >> that, unlike bedGraph, the bed or bigBed format does not support this >> type of display. Is that correct? If so, ideally what I am looking for >> is a way to control the color of the bars and the track label >> separately in a bedGraph (or changing bar colors without affecting label >> color) . >> If that can't be done, I'm considering to maybe switch to using bed >> format with some simple color gradient instead. >> >> Thanks, >> Tien-chi >> >> On Fri, Mar 19, 2010 at 6:22 AM, Jennifer Jackson<[email protected] >> <mailto:[email protected]>> wrote: >> >> Hello again Tien-chi, >> >> There is one more option that uses a new attribute called >> colorByStrand (documentation pending). >> >> This option also requires a data transformation into bed format, but >> only a bed6, not a bed9. It also allows you to avoid using a >> bigDataUrl. An important assumption is that you do not care about >> strand (likely not, as the bedGraph data is not stranded). >> >> Below is an example using the colorByStrand track attribute. Note >> that when used in combination with exonArrows=off, all clues are >> removed from the graphed data that strand was included in the custom >> track source data file. >> >> browser hide all >> track db=hg19 name=strandColor description="colorByStrand testing" >> visibility=pack colorByStrand="255,0,0 0,0,255" exonArrows=off >> chr21 33031597 33041570 itemNegative 1000 - >> chr21 33031597 33041570 itemPositive 1000 + >> >> When loading the example into the Custom track submission page, >> remember to remove any new line returns from the track line that >> result from a copy& paste. Track lines should always be one >> continuous string. >> >> Hopefully one of these solutions will work for your project, >> Jennifer >> >> --------------------------------- >> Jennifer Jackson >> UCSC Genome Informatics Group >> http://genome.ucsc.edu/ >> >> >> On 3/17/10 9:44 PM, Tien-chi Pan wrote: >> >> Hi, >> >> I am using the following track definition line to display copy >> number data >> in two-color BedGraph: >> >> track type="bedGraph" name="Track1" description="Track 1" >> visibility=full >> color=255,0,0 altColor=0,255,0 autoScale=off viewLimits=-2:2 >> >> All is fine except the track label shows up as red due to the color >> parameter setting. The effect I would like to achieve is having >> red bars for >> positive data and green bars for negative data, while the track >> label >> remains black. >> >> Is there a way to set the color of the track label separately >> from the >> colors of the bars? I tried setting itemRgb but it didn't appear >> to work on >> BedGraph. >> >> Thanks, >> Tien-chi >> _______________________________________________ >> Genome maillist - [email protected] >> <mailto:[email protected]> >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
