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
