[Gmod-ajax] Formatting using GFF notes and some other stuff

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[Gmod-ajax] Formatting using GFF notes and some other stuff

David Breimann
Hi,

1. I would like to display some annotations from a GFF file on a single track and control their color/glyph according to the content of the note in the GFF (e.g. if 'Note=red' I would like this feature to be colored red, and if 'Note=green' I would like it to be green).
2. Can  I control for the height of the tracks (I know it can be done for WIG tracks, but what about normal features tracks)?
3. How can I control which tracks are shown by default?
4. Suggestion: have a "reset view" in the browser (currently I have to clear my browser history to return to the default view).
5. Is there any ETA for the improvement of the WIG tracks (most importantly adding a scale)?

Keep up the good work,
Dave

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Re: Formatting using GFF notes and some other stuff

Mitch Skinner
Most of these are pretty high on the to-do list; specifically:

On 07/26/2010 11:24 PM, David Breimann wrote:
> 1. I would like to display some annotations from a GFF file on a
> single track and control their color/glyph according to the content of
> the note in the GFF (e.g. if 'Note=red' I would like this feature to
> be colored red, and if 'Note=green' I would like it to be green).

Adding an option for javascript callbacks to customize feature elements
is on the to-do list.  The way I'm currently envisioning it, you'd be
able to specify a javascript function that would get the HTML element
for the feature, and the feature data (including "Note" if you specified
it in extraData).  Then you'd be able to modify that HTML element
however you wanted based on that data.

> 2. Can  I control for the height of the tracks (I know it can be done
> for WIG tracks, but what about normal features tracks)?

Are you seeing tracks that are too tall, or too short, or both?

On the development branch, the density histograms now have a height
limit.  On the other hand, if the individual features are shown there's
currently no mechanism for limiting the height of the track, although
that's also on the to-do list.

> 3. How can I control which tracks are shown by default?

In index.html, there's a section that looks like this:

            var b = new Browser({
                                    containerID: "GenomeBrowser",
                                    refSeqs: refSeqs,
                                    trackData: trackInfo,
                                    defaultTracks:
"DNA,gene,mRNA,noncodingRNA",
                                    location: queryParams.loc,
                                    tracks: queryParams.tracks,
                                    bookmark: bookmarkCallback
                                });

the "defaultTracks" setting is a comma-separated list of track labels;
those tracks will be shown by default.

> 4. Suggestion: have a "reset view" in the browser (currently I have to
> clear my browser history to return to the default view).

I don't doubt that this is useful for you, but since I don't think I've
heard this requested before, I'm interested in the specifics of the use
case.  What's the context where you want to do this?  And when you want
to go back to the default view, what makes the default better than what
you were looking at before?

For example, you might have two biological questions that you want to
investigate, and each of them might be addressed using a different set
of tracks.  So if you're looking at a bunch of tracks, and you decide
you want to switch all those tracks off and go look at a different set
of tracks, then that's one situation where I can imagine wanting to do
have a "reset view" option.  But I'd like to hear the specifics of your
case.

> 5. Is there any ETA for the improvement of the WIG tracks (most
> importantly adding a scale)?

That's definitely high on the to-do list, but it's tough to estimate a
time, because it'll involve restructuring the code a bit.  And I'm
currently in the middle of dealing with another issue.  But the scale
bar is probably first on the list after this current bug I'm working on.

Mitch

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Re: Formatting using GFF notes and some other stuff

Ian Holmes
On Jul 27, 2010, at 6:30 AM, Mitch Skinner <[hidden email]> wrote:

>
>> 3. How can I control which tracks are shown by default?
>
> In index.html, there's a section that looks like this:
>
>            var b = new Browser({
>                                    containerID: "GenomeBrowser",
>                                    refSeqs: refSeqs,
>                                    trackData: trackInfo,
>                                    defaultTracks:
> "DNA,gene,mRNA,noncodingRNA",
>                                    location: queryParams.loc,
>                                    tracks: queryParams.tracks,
>                                    bookmark: bookmarkCallback
>                                });
>
> the "defaultTracks" setting is a comma-separated list of track labels;
> those tracks will be shown by default.
>
>> 4. Suggestion: have a "reset view" in the browser (currently I have to
>> clear my browser history to return to the default view).
>
> I don't doubt that this is useful for you, but since I don't think I've
> heard this requested before, I'm interested in the specifics of the use
> case.  What's the context where you want to do this?  And when you want
> to go back to the default view, what makes the default better than what
> you were looking at before?
>
> For example, you might have two biological questions that you want to
> investigate, and each of them might be addressed using a different set
> of tracks.  So if you're looking at a bunch of tracks, and you decide
> you want to switch all those tracks off and go look at a different set
> of tracks, then that's one situation where I can imagine wanting to do
> have a "reset view" option.  But I'd like to hear the specifics of your
> case.
>

There's also a mechanism for encoding the displayed track list in the URL, which might be relevant to points 4&5
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Re: Formatting using GFF notes and some other stuff

David Breimann
In reply to this post by David Breimann
6. I noticed that when I click on the glyphs of feature parsed from GFF3 files, the start coordinate shown on the pop-up window is shifted by -1 relative to the actual coordinate written in the GFF file.

On Tue, Jul 27, 2010 at 9:24 AM, David Breimann <[hidden email]> wrote:
Hi,

1. I would like to display some annotations from a GFF file on a single track and control their color/glyph according to the content of the note in the GFF (e.g. if 'Note=red' I would like this feature to be colored red, and if 'Note=green' I would like it to be green).
2. Can  I control for the height of the tracks (I know it can be done for WIG tracks, but what about normal features tracks)?
3. How can I control which tracks are shown by default?
4. Suggestion: have a "reset view" in the browser (currently I have to clear my browser history to return to the default view).
5. Is there any ETA for the improvement of the WIG tracks (most importantly adding a scale)?

Keep up the good work,
Dave


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Re: Formatting using GFF notes and some other stuff

Scott Cain
Hi David,

That's correct; JBrowse, like Chado, uses interbase coordinates, so it
counts the spaces between bases rather than the bases themselves.
This makes all kinds of math easier, as well as make it easier to
unambiguously identify things like insertion and deletion points.

Scott


On Fri, Jul 30, 2010 at 9:22 AM, David Breimann
<[hidden email]> wrote:

> 6. I noticed that when I click on the glyphs of feature parsed from GFF3
> files, the start coordinate shown on the pop-up window is shifted by -1
> relative to the actual coordinate written in the GFF file.
>
> On Tue, Jul 27, 2010 at 9:24 AM, David Breimann <[hidden email]>
> wrote:
>>
>> Hi,
>>
>> 1. I would like to display some annotations from a GFF file on a single
>> track and control their color/glyph according to the content of the note in
>> the GFF (e.g. if 'Note=red' I would like this feature to be colored red, and
>> if 'Note=green' I would like it to be green).
>> 2. Can  I control for the height of the tracks (I know it can be done for
>> WIG tracks, but what about normal features tracks)?
>> 3. How can I control which tracks are shown by default?
>> 4. Suggestion: have a "reset view" in the browser (currently I have to
>> clear my browser history to return to the default view).
>> 5. Is there any ETA for the improvement of the WIG tracks (most
>> importantly adding a scale)?
>>
>> Keep up the good work,
>> Dave
>
>
> ------------------------------------------------------------------------------
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> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of $1 Million in cash or HP Products. Visit us here for more details:
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> Gmod-ajax mailing list
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> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>



--
------------------------------------------------------------------------
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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Re: Formatting using GFF notes and some other stuff

David Breimann
Well, I also always use 0-based coordinates when I program (as is the rule for arrays in java, perl etc.), but for the user interface - I think it's better show coordinates starting from 1 (as is the rule in all biological databases). For example, when looking at some gene of interest, I think the user expects to see the same coordinates as will be shown in genbank, UCSC genome browser etc. Otherwise, this might cause confusion.

Also, I will appreciate a response for my previous message (cluases 1-5, below).

Dave


On Fri, Jul 30, 2010 at 4:27 PM, Scott Cain <[hidden email]> wrote:
Hi David,

That's correct; JBrowse, like Chado, uses interbase coordinates, so it
counts the spaces between bases rather than the bases themselves.
This makes all kinds of math easier, as well as make it easier to
unambiguously identify things like insertion and deletion points.

Scott


On Fri, Jul 30, 2010 at 9:22 AM, David Breimann
<[hidden email]> wrote:
> 6. I noticed that when I click on the glyphs of feature parsed from GFF3
> files, the start coordinate shown on the pop-up window is shifted by -1
> relative to the actual coordinate written in the GFF file.
>
> On Tue, Jul 27, 2010 at 9:24 AM, David Breimann <[hidden email]>
> wrote:
>>
>> Hi,
>>
>> 1. I would like to display some annotations from a GFF file on a single
>> track and control their color/glyph according to the content of the note in
>> the GFF (e.g. if 'Note=red' I would like this feature to be colored red, and
>> if 'Note=green' I would like it to be green).
>> 2. Can  I control for the height of the tracks (I know it can be done for
>> WIG tracks, but what about normal features tracks)?
>> 3. How can I control which tracks are shown by default?
>> 4. Suggestion: have a "reset view" in the browser (currently I have to
>> clear my browser history to return to the default view).
>> 5. Is there any ETA for the improvement of the WIG tracks (most
>> importantly adding a scale)?
>>
>> Keep up the good work,
>> Dave
>
>
> ------------------------------------------------------------------------------
> The Palm PDK Hot Apps Program offers developers who use the
> Plug-In Development Kit to bring their C/C++ apps to Palm for a share
> of $1 Million in cash or HP Products. Visit us here for more details:
> http://p.sf.net/sfu/dev2dev-palm
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>



--
------------------------------------------------------------------------
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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Re: Formatting using GFF notes and some other stuff

Mitch Skinner
On 07/30/2010 06:37 AM, David Breimann wrote:
> Well, I also always use 0-based coordinates when I program (as is the
> rule for arrays in java, perl etc.), but for the user interface - I
> think it's better show coordinates starting from 1 (as is the rule in
> all biological databases). For example, when looking at some gene of
> interest, I think the user expects to see the same coordinates as will
> be shown in genbank, UCSC genome browser etc. Otherwise, this might
> cause confusion.

I've slowly come around to thinking that we will have to support this
unfortunate convention.  UCSC does the same thing; everything is
interbase except the numbers that it shows people.  Hopefully we can
isolate this weirdness to one part of the code, and not have " + 1"
sprinkled all over the place.b

> Also, I will appreciate a response for my previous message (cluases
> 1-5, below).

A few days ago:
http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-tp998491p999264.html

Mitch

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Re: Formatting using GFF notes and some other stuff

David Breimann
That;s wired, those mess sages never reached me.
Regarding the default view: it just that I'm working with many tracks, and sometimes I like to "clean" things up and start from scratch. Then  simply remove them all manually" (drag each track out of the view), but then the list of tracks is a mess (initially, I create it ordered by some logic).
Obviously, some kind of track hierarchy or grouping (like in GBrowse) would be even better).

And thank you for the replies.

On Fri, Jul 30, 2010 at 7:59 PM, Mitch Skinner <[hidden email]> wrote:
On 07/30/2010 06:37 AM, David Breimann wrote:
Well, I also always use 0-based coordinates when I program (as is the rule for arrays in java, perl etc.), but for the user interface - I think it's better show coordinates starting from 1 (as is the rule in all biological databases). For example, when looking at some gene of interest, I think the user expects to see the same coordinates as will be shown in genbank, UCSC genome browser etc. Otherwise, this might cause confusion.

I've slowly come around to thinking that we will have to support this unfortunate convention.  UCSC does the same thing; everything is interbase except the numbers that it shows people.  Hopefully we can isolate this weirdness to one part of the code, and not have " + 1" sprinkled all over the place.b


Also, I will appreciate a response for my previous message (cluases 1-5, below).

A few days ago:
http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-tp998491p999264.html

Mitch


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Re: Formatting using GFF notes and some other stuff

Ian Holmes
David Breimann wrote:
> That;s wired, those mess sages never reached me.

Are you subscribed to the gmod-ajax mailing list? If not, please do so -
  it may be that you can help the next person who has questions.

Ian


>         Also, I will appreciate a response for my previous message
>         (cluases 1-5, below).
>
>
>     A few days ago:
>     http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-tp998491p999264.html
>
>     Mitch


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Re: Formatting using GFF notes and some other stuff

Mitch Skinner
In reply to this post by Mitch Skinner
On 07/30/2010 09:59 AM, Mitch Skinner wrote:
> UCSC does the same thing; everything is
> interbase except the numbers that it shows people.

Even though this means that the text disagrees with the graphic!  For
example,

http://genome.ucsc.edu/cgi-bin/hgTracks?insideX=118&revCmplDisp=0&hgsid=166496530&hgt_doJsCommand=&position=chr21%3A33%2C031%2C934-33%2C031%2C938&hgtgroup_map_close=0&hgtgroup_phenDis_close=1&hgtgroup_genes_close=0&hgtgroup_rna_close=0&hgtgroup_expression_close=0&hgtgroup_regulation_close=0&hgtgroup_compGeno_close=0&hgtgroup_varRep_close=0

The "SOD1" gene in the image clearly starts at 33,031,934, but if you
click on the gene then the page you get says that its coordinates are
"chr21:33,031,935-33,041,241".

I consider this a tragedy.  And it's a source of confusion.  But it does
seem to be an established tragedy.

Mitch


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Re: Formatting using GFF notes and some other stuff

David Breimann
In reply to this post by Ian Holmes
Yes, I am on the mailing list. Now I can also see that the messages were on the digest I received, but they did not reach my directly. I don't even see them in the gmail conversation. Also checked my spam and it's not there... wired.

On Fri, Jul 30, 2010 at 8:29 PM, Ian Holmes <[hidden email]> wrote:
David Breimann wrote:
That;s wired, those mess sages never reached me.

Are you subscribed to the gmod-ajax mailing list? If not, please do so -  it may be that you can help the next person who has questions.

Ian



       Also, I will appreciate a response for my previous message
       (cluases 1-5, below).


   A few days ago:
   http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-tp998491p999264.html

   Mitch



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Re: Formatting using GFF notes and some other stuff

Mitch Skinner
In reply to this post by David Breimann
The reason I asked is because I want to know why you want to start over from scratch.  For example, if you're usually switching between two different tasks, then maybe it would be better to implement a mechanism to enable the user to switch between different track setups, rather than making the user recreate their setup on each switch.  Which is something that other people (Andrew Uzilov, for example) have suggested.

Mitch

On 07/30/2010 10:25 AM, David Breimann wrote:
That;s wired, those mess sages never reached me.
Regarding the default view: it just that I'm working with many tracks, and sometimes I like to "clean" things up and start from scratch. Then  simply remove them all manually" (drag each track out of the view), but then the list of tracks is a mess (initially, I create it ordered by some logic).
Obviously, some kind of track hierarchy or grouping (like in GBrowse) would be even better).

And thank you for the replies.

On Fri, Jul 30, 2010 at 7:59 PM, Mitch Skinner <[hidden email]> wrote:
On 07/30/2010 06:37 AM, David Breimann wrote:
Well, I also always use 0-based coordinates when I program (as is the rule for arrays in java, perl etc.), but for the user interface - I think it's better show coordinates starting from 1 (as is the rule in all biological databases). For example, when looking at some gene of interest, I think the user expects to see the same coordinates as will be shown in genbank, UCSC genome browser etc. Otherwise, this might cause confusion.

I've slowly come around to thinking that we will have to support this unfortunate convention.  UCSC does the same thing; everything is interbase except the numbers that it shows people.  Hopefully we can isolate this weirdness to one part of the code, and not have " + 1" sprinkled all over the place.b


Also, I will appreciate a response for my previous message (cluases 1-5, below).

A few days ago:
http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-tp998491p999264.html

Mitch



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Re: Formatting using GFF notes and some other stuff

David Breimann
I think that different setups can be achieved using the "link", but cleaning things up can't be done (unless clearing the browser's history).

On Thu, Aug 5, 2010 at 1:14 AM, Mitch Skinner <[hidden email]> wrote:
The reason I asked is because I want to know why you want to start over from scratch.  For example, if you're usually switching between two different tasks, then maybe it would be better to implement a mechanism to enable the user to switch between different track setups, rather than making the user recreate their setup on each switch.  Which is something that other people (Andrew Uzilov, for example) have suggested.

Mitch


On 07/30/2010 10:25 AM, David Breimann wrote:
That;s wired, those mess sages never reached me.
Regarding the default view: it just that I'm working with many tracks, and sometimes I like to "clean" things up and start from scratch. Then  simply remove them all manually" (drag each track out of the view), but then the list of tracks is a mess (initially, I create it ordered by some logic).
Obviously, some kind of track hierarchy or grouping (like in GBrowse) would be even better).

And thank you for the replies.

On Fri, Jul 30, 2010 at 7:59 PM, Mitch Skinner <[hidden email]> wrote:
On 07/30/2010 06:37 AM, David Breimann wrote:
Well, I also always use 0-based coordinates when I program (as is the rule for arrays in java, perl etc.), but for the user interface - I think it's better show coordinates starting from 1 (as is the rule in all biological databases). For example, when looking at some gene of interest, I think the user expects to see the same coordinates as will be shown in genbank, UCSC genome browser etc. Otherwise, this might cause confusion.

I've slowly come around to thinking that we will have to support this unfortunate convention.  UCSC does the same thing; everything is interbase except the numbers that it shows people.  Hopefully we can isolate this weirdness to one part of the code, and not have " + 1" sprinkled all over the place.b


Also, I will appreciate a response for my previous message (cluases 1-5, below).

A few days ago:
http://gmod.827538.n3.nabble.com/Gmod-ajax-Formatting-using-GFF-notes-and-some-other-stuff-tp998491p999264.html

Mitch




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Re: Formatting using GFF notes and some other stuff

Mitch Skinner
  On 08/05/2010 03:02 AM, David Breimann wrote:
> I think that different setups can be achieved using the "link", but
> cleaning things up can't be done (unless clearing the browser's history).

You can also use the link mechanism to bookmark a clean setup, right?

I'm not trying to argue against what you're asking for, I'm just trying
to understand what's going on when you want to clean up the set of
active tracks.

Earlier, you said:
> Obviously, some kind of track hierarchy or grouping (like in GBrowse)
> would be even better).

but it's not obvious to me how cleaning up tracks relates to the
hierarchy.  I have a guess, but could you expand on this?

Mitch





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