[Gmod-help] Re: [Gmod-gbrowse] Displaying quantitative data from external sources

[Gang Shi]

Hello Dave,

I have been trying my data on Hapmap website, here is the link of it

http://www.hapmap.org/cgi-perl/gbrowse/hapmap27_B36/

The version of the GBrowse shown at the bottom appears to be 1.69. I 
attached a picture of the track (mytrack_hapmap_169.png).

I also tried it on the GBrowse v1.69 installed on my laptop, which is 
under Windows Vista. The track is also attached (mytrack_laptop_169.png).

Thanks for your many suggestions, I will try them out.

Thanks,
Gang


Dave Clements, GMOD Help Desk wrote:
> Hello Gang,
>
> Can you send a picture of what it looks like when it renders the
> track?  Or, if it s a publicly available GBrowse, can you send the URL
> of the GBrowse instance?  Do you know what version of GBrowse it is?
>
> I tried uploading your data to FlyBase, which is GBrowse 1.68 (I
> believe) and WormBase, which is 1.69.
>
> 1.68 does the entirely wrong thing, drawing it with a generic or segments glyph.
>
> 1.69 does better, but it still isn't pretty.  The scale is drawn
> immediately to the right of the point.  I could not figure out how to
> get the scale drawn on the far right.  You might want to turn scale
> off and put the range in the track name:
> key       = myp (Scale 0-10)
>
> Also, the points look better if you play with the point_symbol and
> point_radius options.
>
> Finally, although this isn't what your data looks like, I played with
> making the features be adjacent, having the first one go from 63 to
> 131 and the second one from 132 to 138, changing the graph_type to
> line, and giving them the same name  I expected this to coalesce the
> two features into a single graph, but instead collision detecting
> kicked in and it stacks them instead of aligns them.  Does anyone have
> an explanation for this?
>
> Thanks,
>
> Dave C.
>
> Was this helpful?  Let us know at http://gmod.org/wiki/Help_Desk_Feedback
>
> Learn more about GMOD at SMBE & Arthropod Genomics:
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>   http://www.k-state.edu/agc/symp2009/seminar.html
>
>
>
> On Tue, Apr 21, 2009 at 2:28 PM, Gang Shi <gang at wubios.wustl.edu> wrote:
>   
>> Greeting!
>>
>> I am recently trying to view my own data in the context of genome, so I
>> tried to generate my data in gff3 format and loaded it with the "add
>> your own tracks" in Gbrowser. I can view something at their locations as
>> a single track, but somehow the quantitative values were not displayed
>> in a x-y plot as I wished. I am sure I must miss something, can some
>> help me out? My gff3 file looks as belows.
>>
>> Thanks,
>> Gang
>>
>>
>> [mydata]
>> feature   = p
>> glyph     = xyplot
>> graph_type = points
>> height    = 50
>> min_score = 0
>> max_score = 10
>> bg_color  = blue
>> scale     = right
>> key       = myp
>> chr1    mystudy    p    10725063    10725063    0.83    .    .
>> Name=rs284277_pheno
>> chr1    mystudy    p    10731132    10731132    1.22    .    .
>> Name=rs880315_pheno
>>
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>>     

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