[Genome] help with custom tracks and colors (useScore)

[Ann Zweig]

Hello David,

	Thanks for your compliments on the browser.

	You are correct, as it is, your track is not displaying colors as you 
hoped.  What is happening is that, because all of your 4 data points are 
displayed as a single item (they all have group=T), they are each taking 
on the color of the first data point in the list (that is, they are all 
using the score=1 to color the item).

	If you would like for each of them to take on a gray-scale color equal 
to their score, you will need to display them as separate items.  All 
data points in the same group will be displayed with the same color.

	Additionally, you do not need to specify a 'color' in the track line 
for this type of track.  Try this to see two items with different colors:

track name="test of colors" description="test of colors" useScore=1
browser position chr7:50000000-50000800
chr7	blah	name	50000001	50000200	1	+	0	T1
chr7	blah	name	50000201	50000400	1	+	0	T1
chr7	blah	name	50000401	50000600	667	+	0	T2
chr7	blah	name	50000601	50000800	667	+	0	T2


	I hope this is helpful.  Please don't hesitate to write back if you 
still have questions.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu



Smith, David wrote:
> Hi guys, thank you for supporting your marvelous tool.  I am having
> trouble with displaying color shading with the useScore=1 tag in the
> track line.  My format is .GFF and I'm on the mouse genome, latest
> build.
> 
> The problem is that all of the colors look to be the same shade for
> different scores (ranged 1-1000) and it doesn't matter if it's black
> (color=0,0,0) or blue (0,60,120).  However, if I add UCSC's GC Percent
> track, I can see all of the different shades of black and gray there.
> 
> Here is some sample code.  I just pasted this into the box where it says
> "Add Custom Tracks" after I "Manage Custom Tracks".  This code neither
> works as a .gff file upload.  Does the genome browser not take .gff
> format for its color shading?  The following code appears as a dark gray
> line in the "test of colors" track.
> 
> track name="test of colors" description="test of colors" useScore=1
> color=0,0,0
> chr7	blah	name	50000001	50000200	1	+
> 0	T
> chr7	blah	name	50000201	50000400	334	+
> 0	T
> chr7	blah	name	50000401	50000600	667	+
> 0	T
> chr7	blah	name	50000601	50000800	1000	+
> 0	T
> 
> Thanks for any help that you can pass along.
> 
> "EMF <COH.ORG>" made the following annotations.
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