[Gmod-ajax] XYPlot style via url

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[Gmod-ajax] XYPlot style via url

Raza
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Re: XYPlot style via url

Colin
Loading the BigWig through the URL works fine for me using some volvox sample_data. I can't be sure what the issue is but can you try the same thing on the volvox sample_data?

<a href="http://localhost/jbrowse/index.html?data=sample_data/json/volvox&amp;addStores={">http://localhost/jbrowse/index.html?data=sample_data/json/volvox&addStores={"url":{"type":"JBrowse/Store/SeqFeature/BigWig","urlTemplate":"http://localhost/jbrowse/sample_data/raw/volvox/volvox_sine.bw"}}&addTracks=[{"label":"URL BigWig","type":"JBrowse/View/Track/Wiggle/XYPlot","store":"url"}]&loc=ctgA:24434..26010&tracks=DNA&highlight=

-Colin


On Fri, Jun 27, 2014 at 10:21 AM, rahmanr <[hidden email]> wrote:
Hello every one,
                           My question is related to XYPlot. I have
managed to addStore and addTrack via url. I add BigWig file on fly
through url, but the problem is that it displays no colors. It just
shows the scale for the bw file. Can anybody suggest, what do to?

In case If I have to do it through url How will I do it?

this is my url,
<a href="http://localhost/JBrowse-1.11.4/index.html?data=sample_data/json/mm10&amp;addStores={" target="_blank">http://localhost/JBrowse-1.11.4/index.html?data=sample_data/json/mm10&addStores={"url":{"type":"JBrowse/Store/SeqFeature/BigWig","urlTemplate"
:"http://localhost/JBrowse-1.11.4/sample_data/raw/mm10/data/a.bam.bw"}}&addTracks=[{"label":"rnaseq","type":
"JBrowse/View/Track/Wiggle/XYPlot","store":"url"}]

thanks in advance

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Re: XYPlot style via url

Raza
Hello Colin,
                My JBrowse instance also showed the BigWig file, but the problem is that it shows no red and blue colours ( not any other colour) IT only shows the scale of be file. Which means that it is working but without style. I want to display it along with style. How would I add style to it via url.

thanks
On 27.06.2014 17:58, Colin wrote:
Loading the BigWig through the URL works fine for me using some volvox sample_data. I can't be sure what the issue is but can you try the same thing on the volvox sample_data?

http://localhost/jbrowse/index.html?data=sample_data/json/volvox&addStores={"url":{"type":"JBrowse/Store/SeqFeature/BigWig","urlTemplate":"http://localhost/jbrowse/sample_data/raw/volvox/volvox_sine.bw"}}&addTracks=[{"label":"URL BigWig","type":"JBrowse/View/Track/Wiggle/XYPlot","store":"url"}]&loc=ctgA:24434..26010&tracks=DNA&highlight=

-Colin


On Fri, Jun 27, 2014 at 10:21 AM, rahmanr <[hidden email]> wrote:
Hello every one,
                           My question is related to XYPlot. I have
managed to addStore and addTrack via url. I add BigWig file on fly
through url, but the problem is that it displays no colors. It just
shows the scale for the bw file. Can anybody suggest, what do to?

In case If I have to do it through url How will I do it?

this is my url,
http://localhost/JBrowse-1.11.4/index.html?data=sample_data/json/mm10&addStores={"url":{"type":"JBrowse/Store/SeqFeature/BigWig","urlTemplate"
:"http://localhost/JBrowse-1.11.4/sample_data/raw/mm10/data/a.bam.bw"}}&addTracks=[{"label":"rnaseq","type":
"JBrowse/View/Track/Wiggle/XYPlot","store":"url"}]

thanks in advance

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
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Re: XYPlot style via url

Raza
Hello,
        I finally found out the problem. It was with
bicolor_pivot option. Actually the mean of my data is 0 (zero). When I set it to Zero, it displays no colors.
and I have multiple tracks to be displayed,therefore I can not provide a constant numeric value for each. What should
be the solution?

thanks 
On 30.06.2014 20:09, Colin wrote:
Hey
Can you look in the javascript console and see if there are any errors?

Normally there aren't many debugging statements outputted by jbrowse, but many times in javascript, when a script "crashes" it produces an error message to the console, and it produces this behavior where it just stops rendering

-Colin


On Mon, Jun 30, 2014 at 5:37 AM, rahmanr <[hidden email]> wrote:
Hello,
        To make things easier, I have attached the screen shot of my screen.
This is my url
http://localhost/JBrowse-1.11.4/index.html?data=sample_data/json/mm10&addStores={"url":{"type":"JBrowse/Store/SeqFeature/BigWig","urlTemplate" :"http://localhost/JBrowse-1.11.4/sample_data/raw/mm10/data/myfile.bw"}}&addTracks=[{"label":"rnaseq","type": "JBrowse/View/Track/Wiggle/XYPlot","store":"url"}]

In the screen shot you can see that I have only a range of values rather then a plot.
Can any body please suggest what could be the issue.
many many thanks



On 30.06.2014 10:23, rahmanr wrote:
Hello Colin,
                My JBrowse instance also showed the BigWig file, but the problem is that it shows no red and blue colours ( not any other colour) IT only shows the scale of be file. Which means that it is working but without style. I want to display it along with style. How would I add style to it via url.

thanks
On <a moz-do-not-send="true" href="tel:27.06.2014%2017" value="+12706201417" target="_blank">27.06.2014 17:58, Colin wrote:
Loading the BigWig through the URL works fine for me using some volvox sample_data. I can't be sure what the issue is but can you try the same thing on the volvox sample_data?

http://localhost/jbrowse/index.html?data=sample_data/json/volvox&addStores={"url":{"type":"JBrowse/Store/SeqFeature/BigWig","urlTemplate":"http://localhost/jbrowse/sample_data/raw/volvox/volvox_sine.bw"}}&addTracks=[{"label":"URL BigWig","type":"JBrowse/View/Track/Wiggle/XYPlot","store":"url"}]&loc=ctgA:24434..26010&tracks=DNA&highlight=

-Colin


On Fri, Jun 27, 2014 at 10:21 AM, rahmanr <[hidden email]> wrote:
Hello every one,
                           My question is related to XYPlot. I have
managed to addStore and addTrack via url. I add BigWig file on fly
through url, but the problem is that it displays no colors. It just
shows the scale for the bw file. Can anybody suggest, what do to?

In case If I have to do it through url How will I do it?

this is my url,
http://localhost/JBrowse-1.11.4/index.html?data=sample_data/json/mm10&addStores={"url":{"type":"JBrowse/Store/SeqFeature/BigWig","urlTemplate"
:"http://localhost/JBrowse-1.11.4/sample_data/raw/mm10/data/a.bam.bw"}}&addTracks=[{"label":"rnaseq","type":
"JBrowse/View/Track/Wiggle/XYPlot","store":"url"}]

thanks in advance

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax






------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
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Re: XYPlot style via url

Colin
I'm still not sure what the problem is. Are you saying that when you manually set the bicolor pivot, that your data displays (more or less) correctly? Because when you say "no colors", I presume that you are saying "it's broken". If the bigwig data displays at all, more or less correctly, then we are getting somewhere.

-Colin


On Tue, Jul 1, 2014 at 5:09 AM, rahmanr <[hidden email]> wrote:
Hello,
        I finally found out the problem. It was with
bicolor_pivot option. Actually the mean of my data is 0 (zero). When I set it to Zero, it displays no colors.
and I have multiple tracks to be displayed,therefore I can not provide a constant numeric value for each. What should
be the solution?

thanks 
On 30.06.2014 20:09, Colin wrote:
Hey
Can you look in the javascript console and see if there are any errors?

Normally there aren't many debugging statements outputted by jbrowse, but many times in javascript, when a script "crashes" it produces an error message to the console, and it produces this behavior where it just stops rendering

-Colin


On Mon, Jun 30, 2014 at 5:37 AM, rahmanr <[hidden email]> wrote:
Hello,
        To make things easier, I have attached the screen shot of my screen.
This is my url
http://localhost/JBrowse-1.11.4/index.html?data=sample_data/json/mm10&addStores={"url":{"type":"JBrowse/Store/SeqFeature/BigWig","urlTemplate" :"http://localhost/JBrowse-1.11.4/sample_data/raw/mm10/data/myfile.bw"}}&addTracks=[{"label":"rnaseq","type": "JBrowse/View/Track/Wiggle/XYPlot","store":"url"}]

In the screen shot you can see that I have only a range of values rather then a plot.
Can any body please suggest what could be the issue.
many many thanks



On 30.06.2014 10:23, rahmanr wrote:
Hello Colin,
                My JBrowse instance also showed the BigWig file, but the problem is that it shows no red and blue colours ( not any other colour) IT only shows the scale of be file. Which means that it is working but without style. I want to display it along with style. How would I add style to it via url.

thanks
On <a href="tel:27.06.2014%2017" value="+12706201417" target="_blank">27.06.2014 17:58, Colin wrote:
Loading the BigWig through the URL works fine for me using some volvox sample_data. I can't be sure what the issue is but can you try the same thing on the volvox sample_data?

http://localhost/jbrowse/index.html?data=sample_data/json/volvox&addStores={"url":{"type":"JBrowse/Store/SeqFeature/BigWig","urlTemplate":"http://localhost/jbrowse/sample_data/raw/volvox/volvox_sine.bw"}}&addTracks=[{"label":"URL BigWig","type":"JBrowse/View/Track/Wiggle/XYPlot","store":"url"}]&loc=ctgA:24434..26010&tracks=DNA&highlight=

-Colin


On Fri, Jun 27, 2014 at 10:21 AM, rahmanr <[hidden email]> wrote:
Hello every one,
                           My question is related to XYPlot. I have
managed to addStore and addTrack via url. I add BigWig file on fly
through url, but the problem is that it displays no colors. It just
shows the scale for the bw file. Can anybody suggest, what do to?

In case If I have to do it through url How will I do it?

this is my url,
http://localhost/JBrowse-1.11.4/index.html?data=sample_data/json/mm10&addStores={"url":{"type":"JBrowse/Store/SeqFeature/BigWig","urlTemplate"
:"http://localhost/JBrowse-1.11.4/sample_data/raw/mm10/data/a.bam.bw"}}&addTracks=[{"label":"rnaseq","type":
"JBrowse/View/Track/Wiggle/XYPlot","store":"url"}]

thanks in advance

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax







------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
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Re: XYPlot style via url

Raza
Hi Colin.
            Thanks for helping me out. The problem is solved now. It was just the scaling issue. I was using the global autoscale before, in which the data ranges was from 0-800,000 and hence my peaks were not being shown at all. Yesterday I tried the local and it works perfectly fine.

thanks

On 01.07.2014 18:53, Colin wrote:
I'm still not sure what the problem is. Are you saying that when you manually set the bicolor pivot, that your data displays (more or less) correctly? Because when you say "no colors", I presume that you are saying "it's broken". If the bigwig data displays at all, more or less correctly, then we are getting somewhere.

-Colin


On Tue, Jul 1, 2014 at 5:09 AM, rahmanr <[hidden email]> wrote:
Hello,
        I finally found out the problem. It was with
bicolor_pivot option. Actually the mean of my data is 0 (zero). When I set it to Zero, it displays no colors.
and I have multiple tracks to be displayed,therefore I can not provide a constant numeric value for each. What should
be the solution?

thanks 
On 30.06.2014 20:09, Colin wrote:
Hey
Can you look in the javascript console and see if there are any errors?

Normally there aren't many debugging statements outputted by jbrowse, but many times in javascript, when a script "crashes" it produces an error message to the console, and it produces this behavior where it just stops rendering

-Colin


On Mon, Jun 30, 2014 at 5:37 AM, rahmanr <[hidden email]> wrote:
Hello,
        To make things easier, I have attached the screen shot of my screen.
This is my url
http://localhost/JBrowse-1.11.4/index.html?data=sample_data/json/mm10&addStores={"url":{"type":"JBrowse/Store/SeqFeature/BigWig","urlTemplate" :"http://localhost/JBrowse-1.11.4/sample_data/raw/mm10/data/myfile.bw"}}&addTracks=[{"label":"rnaseq","type": "JBrowse/View/Track/Wiggle/XYPlot","store":"url"}]

In the screen shot you can see that I have only a range of values rather then a plot.
Can any body please suggest what could be the issue.
many many thanks



On 30.06.2014 10:23, rahmanr wrote:
Hello Colin,
                My JBrowse instance also showed the BigWig file, but the problem is that it shows no red and blue colours ( not any other colour) IT only shows the scale of be file. Which means that it is working but without style. I want to display it along with style. How would I add style to it via url.

thanks
On <a moz-do-not-send="true" href="tel:27.06.2014%2017" value="+12706201417" target="_blank">27.06.2014 17:58, Colin wrote:
Loading the BigWig through the URL works fine for me using some volvox sample_data. I can't be sure what the issue is but can you try the same thing on the volvox sample_data?

http://localhost/jbrowse/index.html?data=sample_data/json/volvox&addStores={"url":{"type":"JBrowse/Store/SeqFeature/BigWig","urlTemplate":"http://localhost/jbrowse/sample_data/raw/volvox/volvox_sine.bw"}}&addTracks=[{"label":"URL BigWig","type":"JBrowse/View/Track/Wiggle/XYPlot","store":"url"}]&loc=ctgA:24434..26010&tracks=DNA&highlight=

-Colin


On Fri, Jun 27, 2014 at 10:21 AM, rahmanr <[hidden email]> wrote:
Hello every one,
                           My question is related to XYPlot. I have
managed to addStore and addTrack via url. I add BigWig file on fly
through url, but the problem is that it displays no colors. It just
shows the scale for the bw file. Can anybody suggest, what do to?

In case If I have to do it through url How will I do it?

this is my url,
http://localhost/JBrowse-1.11.4/index.html?data=sample_data/json/mm10&addStores={"url":{"type":"JBrowse/Store/SeqFeature/BigWig","urlTemplate"
:"http://localhost/JBrowse-1.11.4/sample_data/raw/mm10/data/a.bam.bw"}}&addTracks=[{"label":"rnaseq","type":
"JBrowse/View/Track/Wiggle/XYPlot","store":"url"}]

thanks in advance

------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/gmod-ajax








------------------------------------------------------------------------------
Open source business process management suite built on Java and Eclipse
Turn processes into business applications with Bonita BPM Community Edition
Quickly connect people, data, and systems into organized workflows
Winner of BOSSIE, CODIE, OW2 and Gartner awards
http://p.sf.net/sfu/Bonitasoft
_______________________________________________
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