[Genome] coloring custom wiggle tracks

[Hiram Clawson]

Good Afternoon Bob:

The wigColorBy option works if the named track used for
the color reference is a bed track.  You instead have two wiggle tracks.
What you will need to do is take the wiggle track that you want
to be a reference and create a bed track out of it that has
the two colors.  Aren't the two colors simply the plus and minus
values of the wiggle track ?  You can threshold these values in
the table browser and produce a bed track for the positives, and
a bed track for the negatives.  Set the positive bed items to be on the
positive strand (color) and the negative bed items on the negative
strand (altColor).  Put these twos sets of bed items together into a
single track.  Now use that track as your wigColorBy reference.

--Hiram

On 2006 Dec 07, , at 11:39 AM, Bob Thurman wrote:

> Oops, here's that message about using wigColorBy (that I couldn't apply
> to my situation) --
>
> -----Original Message-----
> From: Hiram Clawson [mailto:hiram at soe.ucsc.edu 
> <http://www.soe.ucsc.edu/mailman/listinfo/genome>]
> Sent: Monday, April 10, 2006 2:16 PM
> To: Ma, Jin
> Cc: 'genome at soe.ucsc.edu 
> <http://www.soe.ucsc.edu/mailman/listinfo/genome>'
> Subject: Re: [Genome] Suggestion on coloring the wiggle track
>
>
> Good Morning Jin:
>
> You can get the wiggle track to color itself based on the contents
> of a different track.  In the trackDb entry for the wiggle track you
> want to color, place the declaration:
> wigColorBy <other track name>
>
> The wiggle will now color itself in the same manner as the other
> track is colored.  The other track is some kind of simple bed track.
> If you create your other bed track item colors in a color scheme
> that indicates your level of significance, then the wiggle track
> will indicate those colors.
>
> --Hiram
>
>
>
> Bob Thurman wrote:
>> Hi,
>>
>> I have a question about coloring custom wiggle tracks.  I have two
>> wiggle tracks, one of which I am coloring with the 'color=' and
>> 'altColor=' options on the track line.  And what I'd like to do is 
>> color
>> the second track using the same color scheme as the first.  I.e., I'd
>> like the 2nd track to be green exactly when the first track is, and to
>> switch to red exactly when the first track does.  Is this possible?
>>
>> I found the message below, which mentions the use of wigColorBy, but 
>> I'm
>> not sure that this is applicable to my situation, and any way, I can't
>> get it to work (when I add 'wigColorBy=track1' in the second track's
>> track line, I get the message "track1 not found", even though the 
>> first
>> track has 'name=track1').
>>
>> Another option I tried was using the 'itemRgb' option on each data 
>> line
>> of the second track, but apparently that is not available for wiggle 
>> track.
>>
>> Thanks for your help.
>>
>> Bob
>>
>>
>
> -- 
> ===========================================================
> Bob Thurman,  Ph.D.                    Research Scientist
> Division of Medical Genetics
> Noble Lab
> J-205 Health Sciences Building
> Box 357720
> University of Washington
> Seattle, WA 98195-7720                 206-543-8916
> ===========================================================