Re: [Gmod-gbrowse] Wiggle Tracks for time-series data (Peter Koppstein)

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Re: [Gmod-gbrowse] Wiggle Tracks for time-series data (Peter Koppstein)

Weeks, Nathan
Gmod-gbrowse Digest, Vol 48, Issue 46
With regard to the first problem: if your wiggle features are named such that their lexicographic ordering is the order you want, you can specify "sort_order = name" in the stanza for the wiggle track; otherwise, you can use a callback; additional info on how to do this with sort_order is in the documentation for Bio::Graphics::Glyph.
 
-- 
Nathan Weeks
Information Technology Specialist
USDA-ARS CICGRU
(515) 294-9777
------------------------------

Message: 2
Date: Tue, 18 May 2010 16:16:51 -0400
From: Peter Koppstein <[hidden email]>
Subject: [Gmod-gbrowse] Wiggle Tracks for time-series data
To: [hidden email]
Cc: Lance Parsons <[hidden email]>, Lincoln Stein
        <[hidden email]>
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset=us-ascii

We have been using GBrowse successfully with several genomes, but are currently unable to resolve two problems related to "wiggle
tracks". In brief, we are having trouble generating the kind of display show at the top of the page:
 http://gmod.org/w/index.php?title=GBrowse/Uploading_Wiggle_Tracks

We are able to display our time-series data as a single "track" consisting of a stack of multiple horizontal "wiggle plots" (one plot per time period). Furthermore, we have been able to do this both by uploading it to the backend database, and by using the "Upload your own data:" feature.

The first problem is that we have not been able to figure out how to get the stack of horizontal "wiggle" plots in the correct temporal
order when using the backend database. This problem does not arise when we use the "Upload your own data:" feature. Further details are given below.

The second problem is that, using the "Upload your own data:" feature, we haven't been able to eliminate any of the three textual lines that
appear for each horizontal plot (that is, in order, the "name", the "ref_sequence" line ("I.data"), and the "description"). Ideally we would like to present the features in the economical way shown in the figure at the top of the Uploading_Wiggle_Tracks page (i.e., with the
caption to the left of the plot).

With thanks for any pointers or hints you may be able to provide,

Peter Koppstein
Scientific Programmer
Lewis-Sigler Institute for Integrative Genomics
Princeton University

[hidden email]
w: 609 258-9104
c: 609 933-5886

GBrowse version: 1.70
Platform: Linux
Perl: 5.8.8

Ordering of the Plots within a Track
====================================

The data was uploaded to the backend database from gff3 files in which
the time is encoded as part of the "source". For example, here in
simplified form are some lines from the gff3 file representing
t=12,18,24,...:

Pf3D7_01 X_12 feature 1 10 . . . .
Pf3D7_01 X_18 feature 1 10 . . . .
Pf3D7_01 X_24 feature 1 10 . . . .
Pf3D7_01 X_30 feature 1 10 . . . .
Pf3D7_01 X_36 feature 1 10 . . . .

For the plots for time = 12, 18, ... 36, the ordering is (from top to bottom):
 24 18 12 30 36




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Re: Wiggle Tracks for time-series data (Peter Koppstein)

Peter Koppstein
On May 18, 2010, at 5:05 PM, Weeks, Nathan wrote:

With regard to the first problem: if your wiggle features are named such that their lexicographic ordering is the order you want, you can specify "sort_order = name" in the stanza for the wiggle track; otherwise, you can use a callback; additional info on how to do this with sort_order is in the documentation for Bio::Graphics::Glyph.

Thanks very much for your detailed help. 

It's curious that the "sort order" parameter isn't documented on the "Uploading WIggle Tracks" page, the "GBrowse Configuration HOWTO" page, or the "Tutorial for Administrators" page..... So I took the plunge and added a subsection at the bottom of the first of these:


Please feel free to make any corrections or improvements!

With thanks again,
Peter

------------------------------

Message: 2
Date: Tue, 18 May 2010 16:16:51 -0400
From: Peter Koppstein <[hidden email]>
Subject: [Gmod-gbrowse] Wiggle Tracks for time-series data
To: [hidden email]
Cc: Lance Parsons <[hidden email]>, Lincoln Stein
        <[hidden email]>
Message-ID:
        <[hidden email]>
Content-Type: text/plain; charset=us-ascii

We have been using GBrowse successfully with several genomes, but are currently unable to resolve two problems related to "wiggle
tracks". In brief, we are having trouble generating the kind of display show at the top of the page:
 http://gmod.org/w/index.php?title=GBrowse/Uploading_Wiggle_Tracks

We are able to display our time-series data as a single "track" consisting of a stack of multiple horizontal "wiggle plots" (one plot per time period). Furthermore, we have been able to do this both by uploading it to the backend database, and by using the "Upload your own data:" feature.

The first problem is that we have not been able to figure out how to get the stack of horizontal "wiggle" plots in the correct temporal
order when using the backend database. This problem does not arise when we use the "Upload your own data:" feature. Further details are given below.

The second problem is that, using the "Upload your own data:" feature, we haven't been able to eliminate any of the three textual lines that
appear for each horizontal plot (that is, in order, the "name", the "ref_sequence" line ("I.data"), and the "description"). Ideally we would like to present the features in the economical way shown in the figure at the top of the Uploading_Wiggle_Tracks page (i.e., with the
caption to the left of the plot).

With thanks for any pointers or hints you may be able to provide,

Peter Koppstein
Scientific Programmer
Lewis-Sigler Institute for Integrative Genomics
Princeton University

[hidden email]
w: 609 258-9104
c: 609 933-5886

GBrowse version: 1.70
Platform: Linux
Perl: 5.8.8

Ordering of the Plots within a Track
====================================

The data was uploaded to the backend database from gff3 files in which
the time is encoded as part of the "source". For example, here in
simplified form are some lines from the gff3 file representing
t=12,18,24,...:

Pf3D7_01 X_12 feature 1 10 . . . .
Pf3D7_01 X_18 feature 1 10 . . . .
Pf3D7_01 X_24 feature 1 10 . . . .
Pf3D7_01 X_30 feature 1 10 . . . .
Pf3D7_01 X_36 feature 1 10 . . . .

For the plots for time = 12, 18, ... 36, the ordering is (from top to bottom):
 24 18 12 30 36





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Re: Wiggle Tracks for time-series data (Peter Koppstein)

Scott Cain
Hi Peter,

Excellent, thank you!

Scott


On Wed, May 19, 2010 at 12:38 PM, Peter Koppstein
<[hidden email]> wrote:

> On May 18, 2010, at 5:05 PM, Weeks, Nathan wrote:
>
> With regard to the first problem: if your wiggle features are named such
> that their lexicographic ordering is the order you want, you can specify
> "sort_order = name" in the stanza for the wiggle track; otherwise, you can
> use a callback; additional info on how to do this with sort_order is in the
> documentation for Bio::Graphics::Glyph.
>
> Thanks very much for your detailed help.
> It's curious that the "sort order" parameter isn't documented on the
> "Uploading WIggle Tracks" page, the "GBrowse Configuration HOWTO" page, or
> the "Tutorial for Administrators" page..... So I took the plunge and added a
> subsection at the bottom of the first of these:
> http://gmod.org/wiki/GBrowse/Uploading_Wiggle_Tracks
> Please feel free to make any corrections or improvements!
> With thanks again,
> Peter
>
> ------------------------------
>
> Message: 2
> Date: Tue, 18 May 2010 16:16:51 -0400
> From: Peter Koppstein <[hidden email]>
> Subject: [Gmod-gbrowse] Wiggle Tracks for time-series data
> To: [hidden email]
> Cc: Lance Parsons <[hidden email]>, Lincoln Stein
>         <[hidden email]>
> Message-ID:
>         <[hidden email]>
> Content-Type: text/plain; charset=us-ascii
>
> We have been using GBrowse successfully with several genomes, but are
> currently unable to resolve two problems related to "wiggle
> tracks". In brief, we are having trouble generating the kind of display show
> at the top of the page:
>  http://gmod.org/w/index.php?title=GBrowse/Uploading_Wiggle_Tracks
>
> We are able to display our time-series data as a single "track" consisting
> of a stack of multiple horizontal "wiggle plots" (one plot per time period).
> Furthermore, we have been able to do this both by uploading it to the
> backend database, and by using the "Upload your own data:" feature.
>
> The first problem is that we have not been able to figure out how to get the
> stack of horizontal "wiggle" plots in the correct temporal
> order when using the backend database. This problem does not arise when we
> use the "Upload your own data:" feature. Further details are given below.
>
> The second problem is that, using the "Upload your own data:" feature, we
> haven't been able to eliminate any of the three textual lines that
> appear for each horizontal plot (that is, in order, the "name", the
> "ref_sequence" line ("I.data"), and the "description"). Ideally we would
> like to present the features in the economical way shown in the figure at
> the top of the Uploading_Wiggle_Tracks page (i.e., with the
> caption to the left of the plot).
>
> With thanks for any pointers or hints you may be able to provide,
>
> Peter Koppstein
> Scientific Programmer
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
>
> [hidden email]
> w: 609 258-9104
> c: 609 933-5886
>
> GBrowse version: 1.70
> Platform: Linux
> Perl: 5.8.8
>
> Ordering of the Plots within a Track
> ====================================
>
> The data was uploaded to the backend database from gff3 files in which
> the time is encoded as part of the "source". For example, here in
> simplified form are some lines from the gff3 file representing
> t=12,18,24,...:
>
> Pf3D7_01 X_12 feature 1 10 . . . .
> Pf3D7_01 X_18 feature 1 10 . . . .
> Pf3D7_01 X_24 feature 1 10 . . . .
> Pf3D7_01 X_30 feature 1 10 . . . .
> Pf3D7_01 X_36 feature 1 10 . . . .
>
> For the plots for time = 12, 18, ... 36, the ordering is (from top to
> bottom):
>  24 18 12 30 36
>
>
>
>
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Gmod-gbrowse mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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