gmod-ajax

Re: [Gmod-ajax] quantitative ("wiggle") tracks do not work

[Mitch S. <mit...@be...>]

Look in your JBrowse instance at chr05 around base 15377500:

http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html?loc=chr05:15373621..15382921

Currently, JBrowse plots wiggle data on a linear scale, and by default
it uses the largest values in the wiggle file to define the top of the
plotted range. You have seen blank-looking images in the places you've
looked because most of your data values are much, much lower than the
maximum values in your dataset. They're so small in the plot that they
don't show up at all.

Right now, one thing you could do is add a --min and --max parameter to
the wig-to-json.pl command line to specify the range of values to plot.
For example, if you specified --min 0 --max 100 then the plot would show
values in that range, and values larger than that would be out-of-range
above the plot.

We've also been talking about adding an option to plot on a logarithmic
vertical scale; would that work for your data? I've looked at histograms
of some next-gen coverage data, and it seems like the distribution of
data values makes sense to plot on a logarithmic scale. But I think the
range of values that is most interesting depends on the biology, and
possibly on how the data is normalized; are you comparing this data to
some kind of control?

Regards,
Mitch

Lianfeng GU wrote:
> Hi prof Mitch:
>
> Thank you for your reply.
>
> After type "make" command in JBrowse root directory
>
> i run "bin/wig-to-json.pl --wig dataset/wig/Col.wig", however i cannot
> see any figure in Col.wig track.
>
> You can check it by following website:
>
> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html

[removed username and password because I'm cc-ing the mailing list. -Mitch]

> When i use your test dataset, the quantitative ("wiggle") tracks work
> well. You can see the Figure in wiggle tracks you can see it by
> following website:
>
> http://bioinfo.genetics.ac.cn/tool/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>
> The file of my Col.wig look like this:
>
> track type=bedGraph name="TopHat - read coverage"
> chr04 0 4051 0
> chr04 4051 4088 1
> chr04 4088 4090 14
> chr04 4090 4093 18
> chr04 4093 4094 20
> chr04 4094 4095 22
> chr04 4095 4096 24
> chr04 4096 4097 25
> chr04 4097 4126 28
> chr04 4126 4130 27
> chr04 4130 4153 28
> chr04 4153 4163 29
> chr04 4163 4165 16
> chr04 4165 4168 12
> chr04 4168 4169 10
>
> I donot know the reason that i cannot get any figure in wiggle tracks.
>
> Thank you for your suggestion and help.
>
> Best wishes
>
> Lianfeng
>
>
>
>

Re: [Gmod-ajax] Question about exact align between different tracks at high resolution

[Mitch S. <mit...@be...>]

lfgu wrote:
> I will take your test dataset to descript this question.
>  
> The exact region for the second exon of rna-Apple3 genes in your volvox.gff3 file is 19000-19500.
>  
> When you press the zoom in button until you can see bases at DNA tracks,then you will find that the Figure for second exon structure in 
> Exonerate predictions tracks is not located from 19000 to 19500. 
>  
> The align between  DNA Tracks and Exonerate predictions tracks is not exact align at single base resolution, 
> there are several bases deviation.
>  
> I also check many cases on my own dataset, it is a pervasive phenomenon.

There are a few things going on here.  One is that some web browsers are 
less accurate than others; ticket #12 is for the JBrowse changes 
required to work around this, which I plan to work on soon (once the 
track density scalability work is done).  Firefox seems more accurate 
than other browsers, so right now you can get somewhat better results 
using that.  What browser are you using?

Another issue is one-based vs. zero-based; we haven't really talked 
about this, so maybe it's a good time to address it.  Currently, JBrowse 
uses interbase coordinates (also known as zero-based, half-open 
coordinates).  Interbase is what the UCSC browser, the chado database, 
and the BED file format use.  The GBrowse genome browser and the GFF 
file format use 1-based, fully closed coordinates.  So the feature that 
starts at "19000" in the GFF file starts one base before "19000" in JBrowse.

For comparison, I've attached screenshots the beginning of a particular 
exon in JBrowse, UCSC, and GBrowse (modENCODE) (the transcript is 
CG42358-RA).  While the numbering is different between the 1-based 
browser and the 0-based browsers, you can see that the DNA sequence and 
the exon boundary line up the same in all of them (with the exon 
starting at the cytosine).

Regards,
Mitch

JBrowse:


UCSC:


GBrowse:

Re: [Gmod-ajax] Question about exact align between different tracks at high resolution

[George G. <geo...@gm...>]

Hi,
Thanks for the efforts in developing Jbrowse.
Please I use  BioRuby for the bulk of my work, At the moment i would like to
embed a jbrowse viewer on a web page for a particular project I am are
working on.  Is there a pure Javascript Jbrowser library/ plugin that i can
use for visualizing GFF files?

Do I have to install bioperl? Are there plans to make Jbrowse bio-language
agnostic?

Thanks!

Re: [Gmod-ajax] Question about exact align between different tracks at high resolution

[Ian H. <ih...@be...>]

Hi George,

Thanks for your interest in & kind comments about JBrowse.

Regarding your question, I'm afraid that currently we don't have any
plans to port or maintain parallel implementations of the server
components in other languages. The idea of a JavaScript implementation
of the server algorithms is interesting, and a Ruby implementation would
certainly be cool too. However JBrowse is a descendant of GBrowse and as
such, will probably continue to use at least some Perl components for a
while (if only to ensure a smooth GBrowse->JBrowse migration path).

It isn't too hard to call Perl scripts from Ruby, though -- right? Would
there be any significant problem with doing that (other than having to
install BioPerl)?

Best wishes,
Ian

George Githinji wrote:
> Hi,
> Thanks for the efforts in developing Jbrowse.
> Please I use  BioRuby for the bulk of my work, At the moment i would like to
> embed a jbrowse viewer on a web page for a particular project I am are
> working on.  Is there a pure Javascript Jbrowser library/ plugin that i can
> use for visualizing GFF files?
> 
> Do I have to install bioperl? Are there plans to make Jbrowse bio-language
> agnostic?
> 
> Thanks!
> 
> 
> 
> ------------------------------------------------------------------------
> 
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
> trial. Simplify your report design, integration and deployment - and focus on 
> what you do best, core application coding. Discover what's new with 
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
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> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] Question about exact align between different tracks at high resolution

[Ian H. <ih...@be...>]

I should also add that there's no reason someone couldn't port the
essential Perl scripts to Ruby. It's not something we plan to maintain
from here, but I think we'd all love to see that, and could offer
advice/help.

Ian Holmes wrote:
> Hi George,
> 
> Thanks for your interest in & kind comments about JBrowse.
> 
> Regarding your question, I'm afraid that currently we don't have any
> plans to port or maintain parallel implementations of the server
> components in other languages. The idea of a JavaScript implementation
> of the server algorithms is interesting, and a Ruby implementation would
> certainly be cool too. However JBrowse is a descendant of GBrowse and as
> such, will probably continue to use at least some Perl components for a
> while (if only to ensure a smooth GBrowse->JBrowse migration path).
> 
> It isn't too hard to call Perl scripts from Ruby, though -- right? Would
> there be any significant problem with doing that (other than having to
> install BioPerl)?
> 
> Best wishes,
> Ian
> 
> George Githinji wrote:
>> Hi,
>> Thanks for the efforts in developing Jbrowse.
>> Please I use  BioRuby for the bulk of my work, At the moment i would like to
>> embed a jbrowse viewer on a web page for a particular project I am are
>> working on.  Is there a pure Javascript Jbrowser library/ plugin that i can
>> use for visualizing GFF files?
>>
>> Do I have to install bioperl? Are there plans to make Jbrowse bio-language
>> agnostic?
>>
>> Thanks!
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
>> trial. Simplify your report design, integration and deployment - and focus on 
>> what you do best, core application coding. Discover what's new with 
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
> 

Re: [Gmod-ajax] quantitative ("wiggle") tracks do not work

[Yuri B. <yrb...@gm...>]

Hi Mitch,
I've used the wiggle track in Gbrowse to plot read coverage and the log
scaling was very useful because like you said the distribution can be wide
(eg, 0-10k).

yuri

On Tue, Sep 1, 2009 at 8:23 PM, Mitch Skinner <mit...@be...>wrote:

> Look in your JBrowse instance at chr05 around base 15377500:
>
>
> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html?loc=chr05:15373621..15382921
>
> Currently, JBrowse plots wiggle data on a linear scale, and by default
> it uses the largest values in the wiggle file to define the top of the
> plotted range. You have seen blank-looking images in the places you've
> looked because most of your data values are much, much lower than the
> maximum values in your dataset. They're so small in the plot that they
> don't show up at all.
>
> Right now, one thing you could do is add a --min and --max parameter to
> the wig-to-json.pl command line to specify the range of values to plot.
> For example, if you specified --min 0 --max 100 then the plot would show
> values in that range, and values larger than that would be out-of-range
> above the plot.
>
> We've also been talking about adding an option to plot on a logarithmic
> vertical scale; would that work for your data? I've looked at histograms
> of some next-gen coverage data, and it seems like the distribution of
> data values makes sense to plot on a logarithmic scale. But I think the
> range of values that is most interesting depends on the biology, and
> possibly on how the data is normalized; are you comparing this data to
> some kind of control?
>
> Regards,
> Mitch
>
> Lianfeng GU wrote:
> > Hi prof Mitch:
> >
> > Thank you for your reply.
> >
> > After type "make" command in JBrowse root directory
> >
> > i run "bin/wig-to-json.pl --wig dataset/wig/Col.wig", however i cannot
> > see any figure in Col.wig track.
> >
> > You can check it by following website:
> >
> >
> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>
> [removed username and password because I'm cc-ing the mailing list. -Mitch]
>
> > When i use your test dataset, the quantitative ("wiggle") tracks work
> > well. You can see the Figure in wiggle tracks you can see it by
> > following website:
> >
> >
> http://bioinfo.genetics.ac.cn/tool/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
> >
> > The file of my Col.wig look like this:
> >
> > track type=bedGraph name="TopHat - read coverage"
> > chr04 0 4051 0
> > chr04 4051 4088 1
> > chr04 4088 4090 14
> > chr04 4090 4093 18
> > chr04 4093 4094 20
> > chr04 4094 4095 22
> > chr04 4095 4096 24
> > chr04 4096 4097 25
> > chr04 4097 4126 28
> > chr04 4126 4130 27
> > chr04 4130 4153 28
> > chr04 4153 4163 29
> > chr04 4163 4165 16
> > chr04 4165 4168 12
> > chr04 4168 4169 10
> >
> > I donot know the reason that i cannot get any figure in wiggle tracks.
> >
> > Thank you for your suggestion and help.
> >
> > Best wishes
> >
> > Lianfeng
> >
> >
> >
> >
>
>
>
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
> trial. Simplify your report design, integration and deployment - and focus
> on
> what you do best, core application coding. Discover what's new with
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> _______________________________________________
> Gmod-ajax mailing list
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>

Re: [Gmod-ajax] quantitative ("wiggle") tracks do not work

[Ian H. <ih...@be...>]

Thanks Yuri.

Mitch, perhaps if the ratio V/R is small enough, where V is the variance
of the data and R=max-min is the range, the logarithmic option should be
triggered automatically?

I.

Yuri Bendana wrote:
> Hi Mitch,
> I've used the wiggle track in Gbrowse to plot read coverage and the log
> scaling was very useful because like you said the distribution can be wide
> (eg, 0-10k).
> 
> yuri
> 
> On Tue, Sep 1, 2009 at 8:23 PM, Mitch Skinner <mit...@be...>wrote:
> 
>> Look in your JBrowse instance at chr05 around base 15377500:
>>
>>
>> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html?loc=chr05:15373621..15382921
>>
>> Currently, JBrowse plots wiggle data on a linear scale, and by default
>> it uses the largest values in the wiggle file to define the top of the
>> plotted range. You have seen blank-looking images in the places you've
>> looked because most of your data values are much, much lower than the
>> maximum values in your dataset. They're so small in the plot that they
>> don't show up at all.
>>
>> Right now, one thing you could do is add a --min and --max parameter to
>> the wig-to-json.pl command line to specify the range of values to plot.
>> For example, if you specified --min 0 --max 100 then the plot would show
>> values in that range, and values larger than that would be out-of-range
>> above the plot.
>>
>> We've also been talking about adding an option to plot on a logarithmic
>> vertical scale; would that work for your data? I've looked at histograms
>> of some next-gen coverage data, and it seems like the distribution of
>> data values makes sense to plot on a logarithmic scale. But I think the
>> range of values that is most interesting depends on the biology, and
>> possibly on how the data is normalized; are you comparing this data to
>> some kind of control?
>>
>> Regards,
>> Mitch
>>
>> Lianfeng GU wrote:
>>> Hi prof Mitch:
>>>
>>> Thank you for your reply.
>>>
>>> After type "make" command in JBrowse root directory
>>>
>>> i run "bin/wig-to-json.pl --wig dataset/wig/Col.wig", however i cannot
>>> see any figure in Col.wig track.
>>>
>>> You can check it by following website:
>>>
>>>
>> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>>
>> [removed username and password because I'm cc-ing the mailing list. -Mitch]
>>
>>> When i use your test dataset, the quantitative ("wiggle") tracks work
>>> well. You can see the Figure in wiggle tracks you can see it by
>>> following website:
>>>
>>>
>> http://bioinfo.genetics.ac.cn/tool/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>>> The file of my Col.wig look like this:
>>>
>>> track type=bedGraph name="TopHat - read coverage"
>>> chr04 0 4051 0
>>> chr04 4051 4088 1
>>> chr04 4088 4090 14
>>> chr04 4090 4093 18
>>> chr04 4093 4094 20
>>> chr04 4094 4095 22
>>> chr04 4095 4096 24
>>> chr04 4096 4097 25
>>> chr04 4097 4126 28
>>> chr04 4126 4130 27
>>> chr04 4130 4153 28
>>> chr04 4153 4163 29
>>> chr04 4163 4165 16
>>> chr04 4165 4168 12
>>> chr04 4168 4169 10
>>>
>>> I donot know the reason that i cannot get any figure in wiggle tracks.
>>>
>>> Thank you for your suggestion and help.
>>>
>>> Best wishes
>>>
>>> Lianfeng
>>>
>>>
>>>
>>>
>>
>>
>> ------------------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
>> trial. Simplify your report design, integration and deployment - and focus
>> on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>> _______________________________________________
>> Gmod-ajax mailing list
>> Gmo...@li...
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
> 
> 
> ------------------------------------------------------------------------
> 
> ------------------------------------------------------------------------------
> Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day 
> trial. Simplify your report design, integration and deployment - and focus on 
> what you do best, core application coding. Discover what's new with 
> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Gmod-ajax mailing list
> Gmo...@li...
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax

Re: [Gmod-ajax] quantitative ("wiggle") tracks do not work

[Brenton G. <brg...@gm...>]

This would be good. But I still think the best option is a dynamic  
scaling based on the max/min in the viewing window even though I  
realize it is difficult to implement. But perhaps having 3 different  
scales of images such as 1-100, 1-1000 and 1-10000 would suffice for  
most cases?

Another feature that would be nice is a scale bar or number to easily  
show the amount of sequence shown in the current window?

Brent

Sent from my iPhone 3GS

On Sep 2, 2009, at 4:41 PM, Ian Holmes <ih...@be...> wrote:

> Thanks Yuri.
>
> Mitch, perhaps if the ratio V/R is small enough, where V is the  
> variance
> of the data and R=max-min is the range, the logarithmic option  
> should be
> triggered automatically?
>
> I.
>
> Yuri Bendana wrote:
>> Hi Mitch,
>> I've used the wiggle track in Gbrowse to plot read coverage and the  
>> log
>> scaling was very useful because like you said the distribution can  
>> be wide
>> (eg, 0-10k).
>>
>> yuri
>>
>> On Tue, Sep 1, 2009 at 8:23 PM, Mitch Skinner <mit...@be... 
>> >wrote:
>>
>>> Look in your JBrowse instance at chr05 around base 15377500:
>>>
>>>
>>> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html?loc=chr05:15373621..15382921
>>>
>>> Currently, JBrowse plots wiggle data on a linear scale, and by  
>>> default
>>> it uses the largest values in the wiggle file to define the top of  
>>> the
>>> plotted range. You have seen blank-looking images in the places  
>>> you've
>>> looked because most of your data values are much, much lower than  
>>> the
>>> maximum values in your dataset. They're so small in the plot that  
>>> they
>>> don't show up at all.
>>>
>>> Right now, one thing you could do is add a --min and --max  
>>> parameter to
>>> the wig-to-json.pl command line to specify the range of values to  
>>> plot.
>>> For example, if you specified --min 0 --max 100 then the plot  
>>> would show
>>> values in that range, and values larger than that would be out-of- 
>>> range
>>> above the plot.
>>>
>>> We've also been talking about adding an option to plot on a  
>>> logarithmic
>>> vertical scale; would that work for your data? I've looked at  
>>> histograms
>>> of some next-gen coverage data, and it seems like the distribution  
>>> of
>>> data values makes sense to plot on a logarithmic scale. But I  
>>> think the
>>> range of values that is most interesting depends on the biology, and
>>> possibly on how the data is normalized; are you comparing this  
>>> data to
>>> some kind of control?
>>>
>>> Regards,
>>> Mitch
>>>
>>> Lianfeng GU wrote:
>>>> Hi prof Mitch:
>>>>
>>>> Thank you for your reply.
>>>>
>>>> After type "make" command in JBrowse root directory
>>>>
>>>> i run "bin/wig-to-json.pl --wig dataset/wig/Col.wig", however i  
>>>> cannot
>>>> see any figure in Col.wig track.
>>>>
>>>> You can check it by following website:
>>>>
>>>>
>>> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>>>
>>> [removed username and password because I'm cc-ing the mailing  
>>> list. -Mitch]
>>>
>>>> When i use your test dataset, the quantitative ("wiggle") tracks  
>>>> work
>>>> well. You can see the Figure in wiggle tracks you can see it by
>>>> following website:
>>>>
>>>>
>>> http://bioinfo.genetics.ac.cn/tool/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>>>> The file of my Col.wig look like this:
>>>>
>>>> track type=bedGraph name="TopHat - read coverage"
>>>> chr04 0 4051 0
>>>> chr04 4051 4088 1
>>>> chr04 4088 4090 14
>>>> chr04 4090 4093 18
>>>> chr04 4093 4094 20
>>>> chr04 4094 4095 22
>>>> chr04 4095 4096 24
>>>> chr04 4096 4097 25
>>>> chr04 4097 4126 28
>>>> chr04 4126 4130 27
>>>> chr04 4130 4153 28
>>>> chr04 4153 4163 29
>>>> chr04 4163 4165 16
>>>> chr04 4165 4168 12
>>>> chr04 4168 4169 10
>>>>
>>>> I donot know the reason that i cannot get any figure in wiggle  
>>>> tracks.
>>>>
>>>> Thank you for your suggestion and help.
>>>>
>>>> Best wishes
>>>>
>>>> Lianfeng
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>> --- 
>>> --- 
>>> --- 
>>> --- 
>>> ------------------------------------------------------------------
>>> Let Crystal Reports handle the reporting - Free Crystal Reports  
>>> 2008 30-Day
>>> trial. Simplify your report design, integration and deployment -  
>>> and focus
>>> on
>>> what you do best, core application coding. Discover what's new with
>>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> Gmo...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>
>>
>> --- 
>> ---------------------------------------------------------------------
>>
>> --- 
>> --- 
>> --- 
>> ---------------------------------------------------------------------
>> Let Crystal Reports handle the reporting - Free Crystal Reports  
>> 2008 30-Day
>> trial. Simplify your report design, integration and deployment -  
>> and focus on
>> what you do best, core application coding. Discover what's new with
>> Crystal Reports now.  http://p.sf.net/sfu/bobj-july
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>
> --- 
> --- 
> --- 
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> 30-Day
> trial. Simplify your report design, integration and deployment - and  
> focus on
> what you do best, core application coding. Discover what's new with
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Re: [Gmod-ajax] quantitative ("wiggle") tracks do not work

[Ian H. <ih...@be...>]

It's considerably more difficult, as the WIG track images are currently
rendered statically. A dynamic scaling would require more track metadata
and Javascript smarts, as opposed to the simpler server tweaks we have
been talking about. But it is do-able and I believe it is on our feature
tracker as something we plan to do.

The scale bar is a very good point; I think that is rather more urgent,
and I hope we'll have that soon

Cheers
I.

Brenton Graveley wrote:
> This would be good. But I still think the best option is a dynamic
> scaling based on the max/min in the viewing window even though I realize
> it is difficult to implement. But perhaps having 3 different scales of
> images such as 1-100, 1-1000 and 1-10000 would suffice for most cases?
> 
> Another feature that would be nice is a scale bar or number to easily
> show the amount of sequence shown in the current window?
> 
> Brent
> 
> Sent from my iPhone 3GS
> 
> On Sep 2, 2009, at 4:41 PM, Ian Holmes <ih...@be...> wrote:
> 
>> Thanks Yuri.
>>
>> Mitch, perhaps if the ratio V/R is small enough, where V is the variance
>> of the data and R=max-min is the range, the logarithmic option should be
>> triggered automatically?
>>
>> I.
>>
>> Yuri Bendana wrote:
>>> Hi Mitch,
>>> I've used the wiggle track in Gbrowse to plot read coverage and the log
>>> scaling was very useful because like you said the distribution can be
>>> wide
>>> (eg, 0-10k).
>>>
>>> yuri
>>>
>>> On Tue, Sep 1, 2009 at 8:23 PM, Mitch Skinner
>>> <mit...@be...>wrote:
>>>
>>>> Look in your JBrowse instance at chr05 around base 15377500:
>>>>
>>>>
>>>> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html?loc=chr05:15373621..15382921
>>>>
>>>>
>>>> Currently, JBrowse plots wiggle data on a linear scale, and by default
>>>> it uses the largest values in the wiggle file to define the top of the
>>>> plotted range. You have seen blank-looking images in the places you've
>>>> looked because most of your data values are much, much lower than the
>>>> maximum values in your dataset. They're so small in the plot that they
>>>> don't show up at all.
>>>>
>>>> Right now, one thing you could do is add a --min and --max parameter to
>>>> the wig-to-json.pl command line to specify the range of values to plot.
>>>> For example, if you specified --min 0 --max 100 then the plot would
>>>> show
>>>> values in that range, and values larger than that would be out-of-range
>>>> above the plot.
>>>>
>>>> We've also been talking about adding an option to plot on a logarithmic
>>>> vertical scale; would that work for your data? I've looked at
>>>> histograms
>>>> of some next-gen coverage data, and it seems like the distribution of
>>>> data values makes sense to plot on a logarithmic scale. But I think the
>>>> range of values that is most interesting depends on the biology, and
>>>> possibly on how the data is normalized; are you comparing this data to
>>>> some kind of control?
>>>>
>>>> Regards,
>>>> Mitch
>>>>
>>>> Lianfeng GU wrote:
>>>>> Hi prof Mitch:
>>>>>
>>>>> Thank you for your reply.
>>>>>
>>>>> After type "make" command in JBrowse root directory
>>>>>
>>>>> i run "bin/wig-to-json.pl --wig dataset/wig/Col.wig", however i cannot
>>>>> see any figure in Col.wig track.
>>>>>
>>>>> You can check it by following website:
>>>>>
>>>>>
>>>> http://bioinfo.genetics.ac.cn/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>>>>
>>>>
>>>> [removed username and password because I'm cc-ing the mailing list.
>>>> -Mitch]
>>>>
>>>>> When i use your test dataset, the quantitative ("wiggle") tracks work
>>>>> well. You can see the Figure in wiggle tracks you can see it by
>>>>> following website:
>>>>>
>>>>>
>>>> http://bioinfo.genetics.ac.cn/tool/jbrowse-jbrowse-fb99d62fd0915a146bbcaa1547b15fd92b2dd7e1/index.html
>>>>
>>>>> The file of my Col.wig look like this:
>>>>>
>>>>> track type=bedGraph name="TopHat - read coverage"
>>>>> chr04 0 4051 0
>>>>> chr04 4051 4088 1
>>>>> chr04 4088 4090 14
>>>>> chr04 4090 4093 18
>>>>> chr04 4093 4094 20
>>>>> chr04 4094 4095 22
>>>>> chr04 4095 4096 24
>>>>> chr04 4096 4097 25
>>>>> chr04 4097 4126 28
>>>>> chr04 4126 4130 27
>>>>> chr04 4130 4153 28
>>>>> chr04 4153 4163 29
>>>>> chr04 4163 4165 16
>>>>> chr04 4165 4168 12
>>>>> chr04 4168 4169 10
>>>>>
>>>>> I donot know the reason that i cannot get any figure in wiggle tracks.
>>>>>
>>>>> Thank you for your suggestion and help.
>>>>>
>>>>> Best wishes
>>>>>
>>>>> Lianfeng
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
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Re: [Gmod-ajax] quantitative ("wiggle") tracks do not work

[Mitch S. <mit...@be...>]

Brenton Graveley wrote:
> This would be good. But I still think the best option is a dynamic 
> scaling based on the max/min in the viewing window even though I 
> realize it is difficult to implement. But perhaps having 3 different 
> scales of images such as 1-100, 1-1000 and 1-10000 would suffice for 
> most cases?

I hear you; I've been thinking about it off and on since you first 
proposed this, but I still don't entirely get it.  So I'd like to go 
into some detail, because I think the answers to these questions will 
help me understand the use case a bit better:

Suppose there is dynamic scaling.  Say you're looking at wiggle data in 
one region where the range of values is 1-100 (plotted, say, 100 pixels 
high), and variation between (say) 80 and 90 is relevant and interesting 
to you.  Now suppose you scroll a teeny bit to the right, and suddenly a 
data value of 10,000 becomes visible.  Then (because of the dynamic 
scaling) the scale changes so that the range of 1-10,000 is plotted on 
the same 100 pixel high region, and now your 80-90 variation is a .1 
pixel difference and is invisible.  Isn't that a problem?

If you're not actually interested in the 80-90 range, then you can plot 
on a 1-10,000 linear scale and be happy.  If you really are interested 
in both 80-90 and also in 8,000-9,000 then you can plot on a log scale 
and be happy.

Is there a specific situation where those two options aren't enough?  It 
seems to me that the point of plotting quantitative data in a genome 
browser is to compare values in one area to values in another area, so 
shouldn't you be able to plot your data all on the same scale?

If you want to call extra attention to really high values we could 
always color them differently or something.  Also, I think it makes 
sense to give the user the option to "zoom" in the y-direction in a 
limited sense.  But given how hard dynamic scaling would be to 
implement, I think it'll be a while before I get to it.  But again, it's 
open source--if someone wants to tackle it I'd be happy to talk about 
how to do it.

> Another feature that would be nice is a scale bar or number to easily 
> show the amount of sequence shown in the current window?

I was just looking at UCSC and I noticed they have both, and GBrowse 
shows the number of bases.  I added a ticket for this.

Regards,
Mitch