[Genome] colour affy?

[Brooke Rhead]

Hi Amanda,

We now have a yellow/blue display option for microarray tracks on our 
test server, at http://genome-test.cse.ucsc.edu/cgi-bin/hgTracks .  The 
option is automatically available on custom microarray tracks.  To turn 
it on, go to the track control page (either by clicking on the blue 
track name, or by clicking the gray or blue "mini-button" to the far 
left of the track display), and look for a radio button to switch from a 
red/green to a yellow/blue display.

Note that our test server also contains many experimental and untested 
tracks.  The option should be on our main server in about a week.  If 
you find any problems with the new yellow/blue functionality, or if you 
have any suggestions for improvement, please let us know!

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Brooke Rhead wrote:
> Hello again Amanda,
> 
> Our developers are working on adding a yellow/blue display option for 
> microarray tracks (including custom tracks) on the main Genome Browser 
> display page.  I will let you know when it is available.
> 
> --
> Brooke Rhead
> UCSC Genome Bioinformatics Group
> 
> 
> Brooke Rhead wrote:
>> Hi Amanda,
>>
>> Ideally, we would have a setting for the main Genome Browser display 
>> (http://genome.ucsc.edu/cgi-bin/hgTracks) to switch microarray tracks so 
>> that they display in yellow/blue instead of red/green, similar to the 
>> settings on the UCSC Genes details pages and the Gene Sorter.  We are 
>> looking into the feasibility of adding that feature.
>>
>> In the meantime, you could experiment with the only settings that we 
>> currently use to control track color and shading: the "useScore"/"color" 
>> track line parameters, or the "itemRgb" column in the BED file.  I'm not 
>> sure if these settings will do much on a microarray custom track.
>>
>> If we are able to implement the yellow/blue to green/red display toggle 
>> in our main Genome Browser display, I will let you know.
>>
>> --
>> Brooke Rhead
>> UCSC Genome Bioinformatics Group
>>
>>
>>
>> Amanda Miotto wrote:
>>> Dear Brooke
>>>
>>> Is there any way around the limitations for shading? Idealy, I was hoping
>>> to have a system that ranged from yellow to blue, similar to the microarray
>>> track, but even a single colour yellow shading would be fantastic. Sorry to
>>> be so fussy, as we are catering for colour-blindness.
>>> Thank you!
>>>
>>>
>>>
>>>
>>> Hello A. Miotto,
>>>
>>> Microarray track coloring is controlled by the "expScale" and "expStep"
>>> parameters. These are described in our genomewiki, here:
>>> http://genomewiki.ucsc.edu/index.php/Microarray_track
>>>
>>> The only colors available for shading based on score are blue, brown,
>>> and black (using the track line parameters "useScore" and "color"):
>>> http://genome.ucsc.edu/goldenPath/help/customTrack.html#TRACK
>>> Also see this previously-answered question on the topic:
>>> http://www.soe.ucsc.edu/pipermail/genome/2005-March/006980.html
>>>
>>> I am not familiar with cURL, but perhaps this section of the User's
>>> Guide that describes constructing URLs to custom tracks will give you
>>> the information you need:
>>> http://genome.ucsc.edu/goldenPath/help/customTrack.html#SHARE
>>> If this does not answer your question, please feel free write back to
>>> the mailing list address.
>>>
>>> I hope this information is helpful.
>>>
>>> --
>>> Brooke Rhead
>>> UCSC Genome Bioinformatics Group
>>>
>>>
>>> Amanda Miotto wrote:
>>>> Dear Sir/Madam
>>>>
>>>> In regards to the genome browser, I am attempting to upload my own tracks
>>>> to view and have some queries:-
>>>> -What parameters are used for colouring the Affy tissue data?
>>>> -Are there any other colours other than blue, black and brown that offer
>>>> shading in a single track?
>>>> -I am trying to write an automated script to upload my tracks
>>> automatically
>>>> to the browser using cURL,
>>>> and was curious on how your browser inputs the filepath for the uploaded
>>>> files using POST in
>>>> your source? Is there a cURL script already available?
>>>>
>>>> Thank you very much for your time.
>>>>
>>>> A.Miotto
>>>>
>>> _______________________________________________
>>> Genome maillist  -  Genome at soe.ucsc.edu
>>> http://www.soe.ucsc.edu/mailman/listinfo/genome
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome