Hi Jennifer
Hmmm... that works for the color but I then lose any ability to display the
'name' attribute on hover.
Also, I don't have control over which color is "on top" (i.e. the connecting
line).
The other element that it would be nice to have some degree of control over is
the appearance of the line which connects the (possibly differently colored)
segments.
I am trying to find good ways to visualize (superimposed) alternate
transcriptional variants using the genome browser....
Any suggestions or examples would be much welcome....
If there is there anything else in the works for color/style control, I would
be happy to learn of it.....
FWIW, I can also code up interleaving colors, i.e.:
browser position chr7:127471000-127471700
browser hide all
track name="ItemRGBDemoInterleaved" description="Item RGB demonstration"
visibility=2 itemRgb="On"
chr7 127471000 127471700 RED 0 + 127471000
127471700 255,0,0 3 100,100,100 0,300,600
chr7 127471100 127471800 GREEN 0 + 127471100
127471800 0,255,0 3 100,100,100 0,300,600
chr7 127471200 127471900 BLUE 0 + 127471200
127471900 0,0,255 3 100,100,100 0,300,600
Thanks,
Malcolm Cook
Stowers Institute for Medical Research - Bioinformatics
Kansas City, Missouri USA
-----Original Message-----
From: Jennifer Jackson [mailto:[email protected]]
Sent: Tuesday, March 23, 2010 1:07 PM
To: Cook, Malcolm
Cc: '[email protected]'; Blanchette, Marco
Subject: Re: [Genome] BedGraph label color
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
