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From: David B. <dav...@gm...> - 2010-07-27 06:25:04
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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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From: Mitch S. <mit...@be...> - 2010-07-27 13:46:21
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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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From: Ian H. <ih...@be...> - 2010-07-27 17:29:43
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On Jul 27, 2010, at 6:30 AM, Mitch Skinner <mit...@be...> 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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From: David B. <dav...@gm...> - 2010-07-30 13:22:44
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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 <dav...@gm...>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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From: Scott C. <sc...@sc...> - 2010-07-30 13:27:17
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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 <dav...@gm...> 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 <dav...@gm...> > 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 > Gmo...@li... > 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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From: David B. <dav...@gm...> - 2010-07-30 13:37:42
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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 <sc...@sc...> 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 > <dav...@gm...> 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 < > dav...@gm...> > > 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 > > Gmo...@li... > > 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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From: Mitch S. <mit...@be...> - 2010-07-30 16:59:47
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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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From: David B. <dav...@gm...> - 2010-07-30 17:25:16
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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 <mit...@be...>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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From: Mitch S. <mit...@be...> - 2010-08-04 22:14:12
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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 > <mit...@be... <mailto:mit...@be...>> 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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From: David B. <dav...@gm...> - 2010-08-05 10:02:49
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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 <mit...@be...>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 <mit...@be... > > 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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From: Mitch S. <mit...@be...> - 2010-07-30 17:35:20
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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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From: Ian H. <ih...@be...> - 2010-07-30 17:29:40
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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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From: David B. <dav...@gm...> - 2010-07-30 18:34:43
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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 <ih...@be...> 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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