display quantitative data in one track with a different glyphs - tiling array

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display quantitative data in one track with a different glyphs - tiling array

guim86

Hi to everybody,

I'm recently using gBrowse and I have a few questions.
I want to display two quantitative data in one track with different glyphs
(ie: points and vertical lines) because I want obtain a graph similar this:
http://www.pnas.org/content/103/14/5320/F1.expansion.html plot  
Any ideas?

Thanks.

Guido

p.s. I think that it is probably necessary to create two wig files:
WIG A -> intensities of my data experiment
WIG B -> with positions where draw the vertical lines
--
View this message in context: http://old.nabble.com/display-quantitative-data-in-one-track-with-a-different-glyphs---tiling-array-tp28662162p28662162.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.


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Re: display quantitative data in one track with a different glyphs - tiling array

Timothy Parnell
I don't think that will be easy to do. In theory you could get the GD object after drawing one glyph on it, and then draw the second glyph on it before writing to an image file and displaying in the browser. That would require digging a bit into the source code.
You best easy alternative might be to display two tracks adjacent to one another, each dependent on separate data sources (e.g. wig or gff files).

Tim
--

Timothy J Parnell, PhD.
Research Associate
Howard Hughes Medical Institute
Department of Oncology
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT 84112



On 5/24/10 3:43 PM, "guim86" <[hidden email]> wrote:



Hi to everybody,

I'm recently using gBrowse and I have a few questions.
I want to display two quantitative data in one track with different glyphs
(ie: points and vertical lines) because I want obtain a graph similar this:
http://www.pnas.org/content/103/14/5320/F1.expansion.html plot
Any ideas?

Thanks.

Guido

p.s. I think that it is probably necessary to create two wig files:
WIG A -> intensities of my data experiment
WIG B -> with positions where draw the vertical lines
--
View this message in context: http://old.nabble.com/display-quantitative-data-in-one-track-with-a-different-glyphs---tiling-array-tp28662162p28662162.html
Sent from the gmod-gbrowse mailing list archive at Nabble.com.


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Re: display quantitative data in one track with a different glyphs - tiling array

Don Gilbert-2-3
In reply to this post by guim86

Guido,

If you are willing to write perl code, you likely can make a glyph draw
the way your example shows. It also may be possible to use this hybrid_plot
glyph to show something like what you want, from two wig files appropriately
loaded with points and vertical bar locations:
  Bio::Graphics::Glyph::hybrid_plot
  An xyplot plot drawing dual graph using data from two wiggle files per track

You might start by creating your WIG A and B files, and test w/ hybrid_plot
to see how close you get, then modify hybrid_plot to get what you want.

= Don Gilbert

|From [hidden email]  Mon May 24 18:20:52 2010
|Date: Mon, 24 May 2010 14:43:45 -0700 (PDT)
|From: guim86 <[hidden email]>
|To: [hidden email]
|X-Nabble-From: [hidden email]
|X-Headers-End: 1OGfR8-00082q-Sd
|X-Mailman-Approved-At: Mon, 24 May 2010 23:19:52 +0000
|Subject: [Gmod-gbrowse] display quantitative data in one track with a
| different glyphs - tiling array
|List-Id: GMOD GBrowse List <gmod-gbrowse.lists.sourceforge.net>
|X-Spam-Level:
|
|
|Hi to everybody,
|
|I'm recently using gBrowse and I have a few questions.
|I want to display two quantitative data in one track with different glyphs
|(ie: points and vertical lines) because I want obtain a graph similar this:
|http://www.pnas.org/content/103/14/5320/F1.expansion.html plot  
|Any ideas?
|
|Thanks.
|
|Guido
|
|p.s. I think that it is probably necessary to create two wig files:
|WIG A -> intensities of my data experiment
|WIG B -> with positions where draw the vertical lines
|--
|View this message in context: http://old.nabble.com/display-quantitative-data-in-one-track-with-a-different-glyphs---tiling-array-tp28662162p28662162.html
|Sent from the gmod-gbrowse mailing list archive at Nabble.com.
|
|
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|_______________________________________________
|Gmod-gbrowse mailing list
|[hidden email]
|https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
|

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