Re: [Gmod-ajax] Graphs

[David B. <dav...@gm...>]

>
> Hi Ian and thanks for the quick reply.
>
> As for #1, thanks for the suggestion. I will look into BigWig.
> As for #2, I would love to get more info about the ImageTrack module.
>
> Let tell you a little bit about how I came to use JBrowse.
> I joined a lab where a couple of standalone (off-line) genome browsers were
> used for a long time. I felt they are really limited so I started looking
> for alternatives.
> GBrowse came up as a leading option, but was a bit disappointed with its
> performance. We use to scroll whole-genomes start to end, so speedy
> scrolling is a must. This was actually almost the single flaw of GBrowse for
> me. If I could only browse faster ("continuously") - it would be great
> (maybe I am missing some trick here?)
>
> I should admit it took me some time to find about JBrowse, but the online
> demonstration was really cool and fast. I am now experiencing with it. My
> first impression is very good, but I feel there are many things missing.
> Some of them are:
> - better interaction: be able to zoom in on selection, export selected
> sequence, use keyboard shortcuts
> - better graphing capabilities (as mentioned in my original post): muktiple
> graphs in the same track, show value when cursor is on graph, show scale
>
> Anyway, I hope you continue the great work and make this great tool even
> better.
>
> Best,
> David
>
>
> On Fri, Jul 2, 2010 at 6:05 PM, Ian Holmes <ih...@be...> wrote:
>
>> Hi David,
>>
>> For #1 do you mean the wig file takes a long time to process, or the
>> resulting image file takes a ling time to load? If the former, yes there is
>> a binary format (BigWig) that could be explored.
>>
>> For #2, the jbrowse client can display any (appropriately processed)
>> image, so it's possible in theory. Our strategy is to develop general
>> software components so that you can write programs on the server yourself to
>> do this. There is, for example, a Perl module that allows you to draw
>> arbitrary graphics primitives onto jbrowse tracks. The particular use case
>> you mentioned (multiple variates on the same plot, using color) is quite a
>> common request and will probably be bundled with jbrowse eventually, but not
>> yet. In the meantime if you are interested in the roll-your-own approach,
>> check out the ImageTrack perl module in the jbrowse source tree. I can send
>> you more info on this if you like.
>>
>> #3 is definitely on our to-do list, near the top.
>>
>> Best wishes
>> Ian
>>
>> On Jul 2, 2010, at 7:51 AM, David Breimann <dav...@gm...>
>> wrote:
>>
>> Hello,
>>
>> I have calculate different scores for each nucleotide in the genome (each
>> score is just a list of numbers which length is the length of the genome). I
>> added a wig header to each score file (fixed step, start = 1, step = 1), and
>> I successfully added such graphs to my JBrowse using
>> <http://wig-to-json.pl>wig-to-json.pl.
>> I have a few questions:
>>
>> 1. Loading these wig file take a long of time. I understand this are heavy
>> graphs, but perhaps there's a better way to present such data other than
>> wig? I guess not, but wonder anyhow.
>>
>> 2. I would like to display a couple of graphs on the same track (different
>> colors). How can this be done? Preferably, the graphs should not be filled
>> (just line plots).
>>
>> 3. I would like to display an axis (ruler) at the edge of the view to get
>> an idea about the values.
>>
>> Is this possible in JBrowse?
>>
>> Thanks,
>> David
>>
>>
>>
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>