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]> 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] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
