[Gmod-ajax] how to modify the bar graph's setting?

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[Gmod-ajax] how to modify the bar graph's setting?

呂怡萱
Hi,
I'm new to use Jbrowse.
Is there any way to get the bar's value?  How to do to save the value into text-file, or show them in the picture, or any way to get it? Thanks in advence.
 
I try to use flatfile-to-json.pl to put my GFF3 data into Jbrowse.
When the data amount is bigger, Jbrowse only shows the bar graph.
The default setting seems no x-axis,y-axis value shown on the track. 
How do I modify the setting, or how to do to get the value ?
Is is possible to save them into the text file? That'll be quite helpful in reading my data. Thank you.
 
Here is the screen shot .
  
 
Regards,
Linda Lu

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Re: how to modify the bar graph's setting?

Mitch Skinner
Hi,

Sorry, but there's currently no way to get those values out of JBrowse.  Can I ask what you want to do with them?  Understanding what people actually want to do is very helpful for deciding how to prioritize work on JBrowse.

We do plan to implement a y-axis scale indicator, which should give a rough idea of what the values are.  But if you want precise values, then of course the scale bar doesn't help very much.  If you just want a few values, then we could implement functionality to show you the number if you click on, or hover over, an individual bar.  But if you want to know all of the values, then obviously that would be very tedious.

If your source data is SAM/BAM, then I believe samtools has some functionality for calculating coverage.  If your source data is in some other format, then there may be other tools that can calculate something similar, but I don't know specifically what you could use.

Mitch

On 08/12/2010 12:56 AM, 呂怡萱 wrote:
Hi,
I'm new to use Jbrowse.
Is there any way to get the bar's value?  How to do to save the value into text-file, or show them in the picture, or any way to get it? Thanks in advence.
 
I try to use flatfile-to-json.pl to put my GFF3 data into Jbrowse.
When the data amount is bigger, Jbrowse only shows the bar graph.
The default setting seems no x-axis,y-axis value shown on the track. 
How do I modify the setting, or how to do to get the value ?
Is is possible to save them into the text file? That'll be quite helpful in reading my data. Thank you.
 

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Re: how to modify the bar graph's setting?

David Breimann
In reply to this post by 呂怡萱
Hi,
 
I read this message at the online archive
and let me comment that I think a y-axis scale indicator as well as display-value-on-mouse-hover is the number one need for me.
Unforutantly I had to quit using JBrowse a couple of weeks ago and postpone my plan to make my database public, since all my numeric tracks are useless without these features implemented. I am currently considering going back to GBrowse or finding some other browser, since I have no idea when these features will be available.
 
Don't misunderstand me - I  love JBrowse and think it will be great, but currently it's missing some essential features, and the uncertainty regarding the future development schedule makes it difficult for me to plan ahead and count on it.
 
Keep up the great work,
Dave

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Re: how to modify the bar graph's setting?

Ian Holmes
David,

We are in the process of initiating formal, version-numbered releases of
JBrowse on a quarterly basis. This should bring our release schedule in
line with the projected development timelines that we provide to NIH.
Consequently, it should allow us to publish more specific forecasts
about the timing of new feature implementations.

The first quarterly release will be in early September, and will focus
on display of high-volume Next Generation Sequencing (NGS) data, along
with a large number of bugfixes.

One of the features you requested, the y-axis scale indicator for
quantitative tracks, narrowly missed our list of targets for the
September release. Instead it will be in the following (December)
release. It remains a high priority, and will likely be one of the first
things we implement after the September release.

So, if you are prepared to continue following this mailing list and
fetching the latest code from github, you could probably get y-axis
scales by early this fall. I can announce this particular feature on
this mailing list when it is ready, if that will help.

In summary, our new release system will, I think, address both the
high-level issues that you raise (concerning the development schedule)
and the specific feature that you cited (reading off y-information from
quantitative tracks). I hope that this will persuade you to persist with
JBrowse a little longer. We remain keen to help you to get the most out
of it.

Best wishes,
Ian


David Breimann wrote:

> Hi,
>  
> I read this message at the online archive
> http://sourceforge.net/mailarchive/message.php?msg_name=4C6BEF8C.9070404%40berkeley.edu
> and let me comment that I think a y-axis scale indicator as well as
> display-value-on-mouse-hover is the number one need for me.
> Unforutantly I had to quit using JBrowse a couple of weeks ago and
> postpone my plan to make my database public, since all my numeric tracks
> are useless without these features implemented. I am currently
> considering going back to GBrowse or finding some other browser, since I
> have no idea when these features will be available.
>  
> Don't misunderstand me - I  love JBrowse and think it will be great, but
> currently it's missing some essential features, and the uncertainty
> regarding the future development schedule makes it difficult for me to
> plan ahead and count on it.
>  
> Keep up the great work,
> Dave
>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Sell apps to millions through the Intel(R) Atom(Tm) Developer Program
> Be part of this innovative community and reach millions of netbook users
> worldwide. Take advantage of special opportunities to increase revenue and
> speed time-to-market. Join now, and jumpstart your future.
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>
>
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Re: how to modify the bar graph's setting?

David Breimann
I will certainly keep tracking JBrowse since I really like it. I hope it will soon catch up with GBrowse and other popular browsers so I could migrate and use it as a first choice.

On Wed, Aug 25, 2010 at 11:57 PM, Ian Holmes <[hidden email]> wrote:
David,

We are in the process of initiating formal, version-numbered releases of JBrowse on a quarterly basis. This should bring our release schedule in line with the projected development timelines that we provide to NIH. Consequently, it should allow us to publish more specific forecasts about the timing of new feature implementations.

The first quarterly release will be in early September, and will focus on display of high-volume Next Generation Sequencing (NGS) data, along with a large number of bugfixes.

One of the features you requested, the y-axis scale indicator for quantitative tracks, narrowly missed our list of targets for the September release. Instead it will be in the following (December) release. It remains a high priority, and will likely be one of the first things we implement after the September release.

So, if you are prepared to continue following this mailing list and fetching the latest code from github, you could probably get y-axis scales by early this fall. I can announce this particular feature on this mailing list when it is ready, if that will help.

In summary, our new release system will, I think, address both the high-level issues that you raise (concerning the development schedule) and the specific feature that you cited (reading off y-information from quantitative tracks). I hope that this will persuade you to persist with JBrowse a little longer. We remain keen to help you to get the most out of it.

Best wishes,
Ian


David Breimann wrote:
Hi,
 I read this message at the online archive
http://sourceforge.net/mailarchive/message.php?msg_name=4C6BEF8C.9070404%40berkeley.edu
and let me comment that I think a y-axis scale indicator as well as display-value-on-mouse-hover is the number one need for me.
Unforutantly I had to quit using JBrowse a couple of weeks ago and postpone my plan to make my database public, since all my numeric tracks are useless without these features implemented. I am currently considering going back to GBrowse or finding some other browser, since I have no idea when these features will be available.
 Don't misunderstand me - I  love JBrowse and think it will be great, but currently it's missing some essential features, and the uncertainty regarding the future development schedule makes it difficult for me to plan ahead and count on it.
 Keep up the great work,
Dave


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