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Gbrowse2 : BigWigSet display

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Christelle Dantec

Gbrowse2 : BigWigSet display

Hi,

I use Bio::DB::BigWigSet adaptator and I am able to see the 2 files in
two differents subtracks. Nevertheless I would like to see them in only
one track automatically.
For the moment, I can display my 2 files in one track by choosing the "
Semi-transparent overlap" option in the configure panel.
Is there a way to configure this option in the .conf ?
I join a screenshot of what I would expect 'automatically'

Could some one have some suggestions?
Thanks by advance

Chris

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Lincoln Stein

Re: Gbrowse2 : BigWigSet display

Hi Christelle,

It isn't obvious, but you can add the following in the track config to get what you want:

bump = overlap

color_series = 1

(this is documented in Bio::Graphics::Panel, but the documentation hasn't propagated into the GBrowse docs)

Let me know if you find any problems with this.

Lincoln

On Thu, Aug 9, 2012 at 6:54 AM, Christelle Dantec <[hidden email]> wrote:

Hi,

I use Bio::DB::BigWigSet adaptator and I am able to see the 2 files in
two differents subtracks. Nevertheless I would like to see them in only
one track automatically.
For the moment, I can display my 2 files in one track by choosing the "
Semi-transparent overlap" option in the configure panel.
Is there a way to configure this option in the .conf ?
I join a screenshot of what I would expect 'automatically'

Could some one have some suggestions?
Thanks by advance

Chris

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
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--
Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

------------------------------------------------------------------------------
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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Timothy Parnell

Re: Gbrowse2 : BigWigSet display

In reply to this post by Christelle Dantec

Hi Chris,

This isn't documented very well (if at all for xyplot glyphs), but these are the options you want to add.

bump = overlap
allows the glyphs, in this case, xyplot style glyphs, to overlap each other

color_series = 1
Tells the glyph to rotate the fgcolor of each item. The default list is found in Bio::Graphics::Glyph::track (I believe) and is "red blue green yellow orange brown aqua black fuchsia green lime maroon navy olive purple silver teal magenta". One thing to note, is that these are not transparent. To make them transparent, define your own list.

color_cycle = red:0.8 blue:0.8
You can define your own color list with this option, space delimited.
To set the transparency, add a colon and fraction number after the color name. So the above color names each have 80% transparency.

One other thing to note. This works best with wiggle_xyplot glyph, not so well with the wiggle_whiskers glyph.

Hope that helps.
Tim

On Aug 9, 2012, at 4:54 AM, Christelle Dantec wrote:

> Hi,
>
> I use Bio::DB::BigWigSet adaptator and I am able to see the 2 files in
> two differents subtracks. Nevertheless I would like to see them in only
> one track automatically.
> For the moment, I can display my 2 files in one track by choosing the "
> Semi-transparent overlap" option in the configure panel.
> Is there a way to configure this option in the .conf ?
> I join a screenshot of what I would expect 'automatically'
>
> Could some one have some suggestions?
> Thanks by advance
>
> Chris
>
>
>
> <wanted.jpeg>------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

Christelle Dantec

Re: Gbrowse2 : BigWigSet display

Wonderful!
Thanks a lot Tim and Lincoln!

Chris

Le jeudi 09 août 2012 à 16:31 +0000, Timothy Parnell a écrit :

> Hi Chris,
>
> This isn't documented very well (if at all for xyplot glyphs), but these are the options you want to add.
>
> bump = overlap
> allows the glyphs, in this case, xyplot style glyphs, to overlap each other
>
> color_series = 1
> Tells the glyph to rotate the fgcolor of each item. The default list is found in Bio::Graphics::Glyph::track (I believe) and is "red blue green yellow orange brown aqua black fuchsia green lime maroon navy olive purple silver teal magenta". One thing to note, is that these are not transparent. To make them transparent, define your own list.
>
> color_cycle = red:0.8 blue:0.8
> You can define your own color list with this option, space delimited.
> To set the transparency, add a colon and fraction number after the color name. So the above color names each have 80% transparency.
>
> One other thing to note. This works best with wiggle_xyplot glyph, not so well with the wiggle_whiskers glyph.
>
> Hope that helps.
> Tim
>
> On Aug 9, 2012, at 4:54 AM, Christelle Dantec wrote:
>
> > Hi,
> >
> > I use Bio::DB::BigWigSet adaptator and I am able to see the 2 files in
> > two differents subtracks. Nevertheless I would like to see them in only
> > one track automatically.
> > For the moment, I can display my 2 files in one track by choosing the "
> > Semi-transparent overlap" option in the configure panel.
> > Is there a way to configure this option in the .conf ?
> > I join a screenshot of what I would expect 'automatically'
> >
> > Could some one have some suggestions?
> > Thanks by advance
> >
> > Chris
> >
> >
> >
> > <wanted.jpeg>------------------------------------------------------------------------------
> > Live Security Virtual Conference
> > Exclusive live event will cover all the ways today's security and
> > threat landscape has changed and how IT managers can respond. Discussions
> > will include endpoint security, mobile security and the latest in malware
> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
> > Gmod-gbrowse mailing list
> > [hidden email]
> > https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>