Re: JBrowse mRNA visualization style

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Re: JBrowse mRNA visualization style

Scott Cain
Hi Leo,

The "3d" appearance of the glyphs comes from a plugin that ships with JBrowse 1.12, one each for canvas and html features, called 'NeatCanvasFeatures' and 'NeatHTMLFeatures'.  To turn them on, add a section like this to you trackList.json file:

    "plugins": [
        'NeatHTMLFeatures',
        'NeatCanvasFeatures'
    ],

That bit of json would go at the same level as the "tracks" section.

I cc'ed this to the JBrowse mailing list in case anybody wants to chime in.

Scott


On Thu, Mar 17, 2016 at 5:27 PM, Leo He <[hidden email]> wrote:
Hi Scott Cain

JBrowser  is a really nice/fast genome browser.
Currently, I'm trying to integrating it into our software.
Here is my question:

How can I get the something like this in your volvox sample (like HTMLFeature -mRNAs or CanvasFeatures - transcripts):
Inline image 2

I used flatfile-to-json.pl --gff  .... command to input a small gff3 file (see bellow) to JBrowser (1.12.1).

chr1    exonerate  mRNA   17400  23000  .  +  .  ID=rna-Apple3;Name=Apple3;Note=mRNA with both CDSs and UTRs
chr1 exonerate UTR 17400 17999 . + . Parent=rna-Apple3
chr1 exonerate CDS 18000 18800 . + 0 Parent=rna-Apple3
chr1 exonerate CDS 19000 19500 . + 1 Parent=rna-Apple3
chr1 exonerate CDS 21000 21200 . + 2 Parent=rna-Apple3
chr1 exonerate UTR 21201 23000 . + . Parent=rna-Apple3
Here is the track canvasFeatures config
{
"autocomplete" : "all",
"key" : "test_gff3",
"label" : "test_gff3",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"compress" : 0,
"urlTemplate" : "tracks/test_gff3/{refseq}/trackData.json",
"type" : "CanvasFeatures",
}
}Here is the CanvasFeatures  result
Inline image 1

{
"autocomplete" : "all",
"key" : "test_gff3",
"label" : "test_gff3",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"compress" : 0,
"urlTemplate" : "tracks/test_gff3/{refseq}/trackData.json",
"type" : "HTMLFeatures",
"class" : "mRNAs",
"style" : {
"className" : "mRNA",
"subfeatureClasses" : {
"UTR" : "UTR",
"CDS" : "CDS",
"exon" : "container-100pct",
"wholeCDS" : null
},
"arrowheadClass" : "trellis-arrowhead"
},
}
}Here is the HTMFeatures result
Inline image 3


I spend several days on it but fail to solve the problem.
Could you give me some suggestions for that?

Thank you so much!

Leo







--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: JBrowse mRNA visualization style

Sofia Robb
Thanks Scott! This is pretty!

On Fri, Mar 18, 2016 at 8:05 AM, Scott Cain <[hidden email]> wrote:
Hi Leo,

The "3d" appearance of the glyphs comes from a plugin that ships with JBrowse 1.12, one each for canvas and html features, called 'NeatCanvasFeatures' and 'NeatHTMLFeatures'.  To turn them on, add a section like this to you trackList.json file:

    "plugins": [
        'NeatHTMLFeatures',
        'NeatCanvasFeatures'
    ],

That bit of json would go at the same level as the "tracks" section.

I cc'ed this to the JBrowse mailing list in case anybody wants to chime in.

Scott


On Thu, Mar 17, 2016 at 5:27 PM, Leo He <[hidden email]> wrote:
Hi Scott Cain

JBrowser  is a really nice/fast genome browser.
Currently, I'm trying to integrating it into our software.
Here is my question:

How can I get the something like this in your volvox sample (like HTMLFeature -mRNAs or CanvasFeatures - transcripts):
Inline image 2

I used flatfile-to-json.pl --gff  .... command to input a small gff3 file (see bellow) to JBrowser (1.12.1).

chr1    exonerate  mRNA   17400  23000  .  +  .  ID=rna-Apple3;Name=Apple3;Note=mRNA with both CDSs and UTRs
chr1 exonerate UTR 17400 17999 . + . Parent=rna-Apple3
chr1 exonerate CDS 18000 18800 . + 0 Parent=rna-Apple3
chr1 exonerate CDS 19000 19500 . + 1 Parent=rna-Apple3
chr1 exonerate CDS 21000 21200 . + 2 Parent=rna-Apple3
chr1 exonerate UTR 21201 23000 . + . Parent=rna-Apple3
Here is the track canvasFeatures config
{
"autocomplete" : "all",
"key" : "test_gff3",
"label" : "test_gff3",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"compress" : 0,
"urlTemplate" : "tracks/test_gff3/{refseq}/trackData.json",
"type" : "CanvasFeatures",
}
}Here is the CanvasFeatures  result
Inline image 1

{
"autocomplete" : "all",
"key" : "test_gff3",
"label" : "test_gff3",
"storeClass" : "JBrowse/Store/SeqFeature/NCList",
"compress" : 0,
"urlTemplate" : "tracks/test_gff3/{refseq}/trackData.json",
"type" : "HTMLFeatures",
"class" : "mRNAs",
"style" : {
"className" : "mRNA",
"subfeatureClasses" : {
"UTR" : "UTR",
"CDS" : "CDS",
"exon" : "container-100pct",
"wholeCDS" : null
},
"arrowheadClass" : "trellis-arrowhead"
},
}
}Here is the HTMFeatures result
Inline image 3


I spend several days on it but fail to solve the problem.
Could you give me some suggestions for that?

Thank you so much!

Leo







--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785231&iu=/4140
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax



------------------------------------------------------------------------------
Transform Data into Opportunity.
Accelerate data analysis in your applications with
Intel Data Analytics Acceleration Library.
Click to learn more.
http://pubads.g.doubleclick.net/gampad/clk?id=278785351&iu=/4140
_______________________________________________
Gmod-ajax mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-ajax