[Gmod-ajax] Graphs

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[Gmod-ajax] Graphs

David Breimann
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 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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Re: Graphs

Ian Holmes
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 <[hidden email]> 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 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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Re: Graphs

David Breimann
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 <[hidden email]> 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
IanĀ 

On Jul 2, 2010, at 7:51 AM, David Breimann <[hidden email]> 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 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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