Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Fixed
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Labels:None
Description
Please re-assign (or not) as you see fit.
This is a new feature request and I know it's getting late in the game. But if you could slip it in without risking too many bugs, I would appreciate it!
BED file has "rgb" filed, which is comma-separated red, green, blue values.
If a BED file contains data in this field, please color the corresponding Glyphs using the designated RGB values.
All other Glyphs would be colored using the default colors or whatever is specified in annots.xml, if there is one.
If user selects a track and uses the color swatches or change foreground command, then all the Glyphs should change to the new color. If user resets to default, then the original colors should be restored, determined by the RGB field in cases where that field was set.
We need this to color-code annotation types. We have started updating Arabidopsis and rice gene models and want to use color to indicate revision status and types of revisions.
Attachments
Issue Links
- relates to
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BUG-622 File format issues
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- Closed
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Activity
I need a file which has this information in it (or at least the range of a file) to test.
You can create one using one of the TAIR10 files.
Hand-edit the RGB field.
Test a file that has multiple colors set and which also has no colors set using the RGB field.
Create one using a a BED file checked out from QL and hand-edit following the BED spec described in the UCSC FAQ. (Find it by google-searching "UCSC BED format.")
To get part of a file, do this:
$ gunzip -c FILE.bed.gz > SAMPLE.bed
then open in a text editor and edit.
Be sure to include lines in which the RGB is not set as well as lines that are.
"at column 9 itemRgb - An RGB value of the form R,G,B (e.g. 255,0,0). If the track line itemRgb attribute is set to "On", this RBG value will determine the display color of the data contained in this BED line. NOTE: It is recommended that a simple color scheme (eight colors or less) be used with this attribute to avoid overwhelming the color resources of the Genome Browser and your Internet browser."
Attached is a 2 line bed file for chr 2 of A thal. It loads the two items, but they are the default color, not the adjusted colors (notice that the colors are set as 255,0,0 and 0,255,0).
So this is not working.
It requires a track line
track name="Bed Test File" description="Test bed file" color=255,255,0 itemRgb="on" useScore=0 url="http://www.google.com/search?q=$$"
(try new attachment)
Do you want to always turn it on irrespective of itemRgb value?
Load A thal, chr2. Load the larger file (.5kb). See that there is a red mark aoe and a green mark below. Change the color of the track - the marks should now match the FG color. Use Anntotations tab and 'restore default' to track. The red and green should reappear.
Done in r13426-13432.