[Gmod-ajax] Modification to Gene.js; general interest?

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[Gmod-ajax] Modification to Gene.js; general interest?

Scott Cain
Hi All,

I just wanted to throw this out there: I recently ran into a problem where we have genes that have both mRNAs as well as non-coding transcripts in it (annotated as nc_primary_transcript in the GFF).  Unfortunately, the gene glyph doesn't know what to do with the non-coding but still spliced transcripts and just draws a box glyph for them.  To rectify this situation, I did a little hacking on the gene glyph:


which in turn depends on a new transcript glyph: 


WBGene.js is very similar to the original Gene.js, except that it allows for a "main" transcript type (the first in the comma separated list of transcript types) and minor transcript types (any of the rest of SO types in the list), with the implicit assumption that the first item in the list would be mRNA and the rest would be "something else."  The result looks like the attached screenshot, where the grey transcript is the non-coding one.

Here's what I'm wondering: is there any general interest in this addition?  I'm a few releases behind (1.11.6), so to properly give a pull request for these changes, I'd have to spend some time setting up a dev instance and testing that this additional is robust and sufficiently generic.

Thanks,
Scott


--
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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: Modification to Gene.js; general interest?

Monica Poelchau
Hi Scott,

This looks great - we have been looking for a way to render different feature types within the same track for a while now using HTMLFeatures (in Apollo). Do you think some of the hacks that you did to Gene.js could also be applied to work for HTMLFeatures, at least conceptually?
 
Thanks!

Monica

On Mon, Nov 21, 2016 at 1:01 PM, Scott Cain <[hidden email]> wrote:
Hi All,

I just wanted to throw this out there: I recently ran into a problem where we have genes that have both mRNAs as well as non-coding transcripts in it (annotated as nc_primary_transcript in the GFF).  Unfortunately, the gene glyph doesn't know what to do with the non-coding but still spliced transcripts and just draws a box glyph for them.  To rectify this situation, I did a little hacking on the gene glyph:


which in turn depends on a new transcript glyph: 


WBGene.js is very similar to the original Gene.js, except that it allows for a "main" transcript type (the first in the comma separated list of transcript types) and minor transcript types (any of the rest of SO types in the list), with the implicit assumption that the first item in the list would be mRNA and the rest would be "something else."  The result looks like the attached screenshot, where the grey transcript is the non-coding one.

Here's what I'm wondering: is there any general interest in this addition?  I'm a few releases behind (1.11.6), so to properly give a pull request for these changes, I'd have to spend some time setting up a dev instance and testing that this additional is robust and sufficiently generic.

Thanks,
Scott


--
------------------------------------------------------------------------
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: Modification to Gene.js; general interest?

Scott Cain
Hi Monica,

I work entirely with canvas features, so I can't say for sure, but my guess is it would work fine--I don't think I did anything that is Canvas-specific.

Scott


On Mon, Nov 21, 2016 at 3:52 PM, Monica Poelchau <[hidden email]> wrote:
Hi Scott,

This looks great - we have been looking for a way to render different feature types within the same track for a while now using HTMLFeatures (in Apollo). Do you think some of the hacks that you did to Gene.js could also be applied to work for HTMLFeatures, at least conceptually?
 
Thanks!

Monica

On Mon, Nov 21, 2016 at 1:01 PM, Scott Cain <[hidden email]> wrote:
Hi All,

I just wanted to throw this out there: I recently ran into a problem where we have genes that have both mRNAs as well as non-coding transcripts in it (annotated as nc_primary_transcript in the GFF).  Unfortunately, the gene glyph doesn't know what to do with the non-coding but still spliced transcripts and just draws a box glyph for them.  To rectify this situation, I did a little hacking on the gene glyph:


which in turn depends on a new transcript glyph: 


WBGene.js is very similar to the original Gene.js, except that it allows for a "main" transcript type (the first in the comma separated list of transcript types) and minor transcript types (any of the rest of SO types in the list), with the implicit assumption that the first item in the list would be mRNA and the rest would be "something else."  The result looks like the attached screenshot, where the grey transcript is the non-coding one.

Here's what I'm wondering: is there any general interest in this addition?  I'm a few releases behind (1.11.6), so to properly give a pull request for these changes, I'd have to spend some time setting up a dev instance and testing that this additional is robust and sufficiently generic.

Thanks,
Scott


--
------------------------------------------------------------------------
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

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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: Modification to Gene.js; general interest?

Eric Yao
Thanks Scott,
It looks good.
If there is concern about general impact, my inclination would be to surface it as a plugin.
This, of course, presents some addition development overhead.

From what I can see, I think some of this could be lang.extend "intercepts" into gene.js.
The NeatCanvasFeatures plugin would be a good example.

Eric


On Mon, Nov 21, 2016 at 1:14 PM, Scott Cain <[hidden email]> wrote:
Hi Monica,

I work entirely with canvas features, so I can't say for sure, but my guess is it would work fine--I don't think I did anything that is Canvas-specific.

Scott


On Mon, Nov 21, 2016 at 3:52 PM, Monica Poelchau <[hidden email]> wrote:
Hi Scott,

This looks great - we have been looking for a way to render different feature types within the same track for a while now using HTMLFeatures (in Apollo). Do you think some of the hacks that you did to Gene.js could also be applied to work for HTMLFeatures, at least conceptually?
 
Thanks!

Monica

On Mon, Nov 21, 2016 at 1:01 PM, Scott Cain <[hidden email]> wrote:
Hi All,

I just wanted to throw this out there: I recently ran into a problem where we have genes that have both mRNAs as well as non-coding transcripts in it (annotated as nc_primary_transcript in the GFF).  Unfortunately, the gene glyph doesn't know what to do with the non-coding but still spliced transcripts and just draws a box glyph for them.  To rectify this situation, I did a little hacking on the gene glyph:


which in turn depends on a new transcript glyph: 


WBGene.js is very similar to the original Gene.js, except that it allows for a "main" transcript type (the first in the comma separated list of transcript types) and minor transcript types (any of the rest of SO types in the list), with the implicit assumption that the first item in the list would be mRNA and the rest would be "something else."  The result looks like the attached screenshot, where the grey transcript is the non-coding one.

Here's what I'm wondering: is there any general interest in this addition?  I'm a few releases behind (1.11.6), so to properly give a pull request for these changes, I'd have to spend some time setting up a dev instance and testing that this additional is robust and sufficiently generic.

Thanks,
Scott


--
------------------------------------------------------------------------
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

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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

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Re: Modification to Gene.js; general interest?

nathandunn
In reply to this post by Monica Poelchau

Monica,

I don’t think Scott’s stuff will necessarily help you for features. 

However, you can already do this I think with the web apollo tracks using css, but editing the appropriate entries here (e.g., ncRNA):


Nathan

On Nov 21, 2016, at 12:52 PM, Monica Poelchau <[hidden email]> wrote:

Hi Scott,

This looks great - we have been looking for a way to render different feature types within the same track for a while now using HTMLFeatures (in Apollo). Do you think some of the hacks that you did to Gene.js could also be applied to work for HTMLFeatures, at least conceptually?
 
Thanks!

Monica

On Mon, Nov 21, 2016 at 1:01 PM, Scott Cain <[hidden email]> wrote:
Hi All,

I just wanted to throw this out there: I recently ran into a problem where we have genes that have both mRNAs as well as non-coding transcripts in it (annotated as nc_primary_transcript in the GFF).  Unfortunately, the gene glyph doesn't know what to do with the non-coding but still spliced transcripts and just draws a box glyph for them.  To rectify this situation, I did a little hacking on the gene glyph:


which in turn depends on a new transcript glyph: 


WBGene.js is very similar to the original Gene.js, except that it allows for a "main" transcript type (the first in the comma separated list of transcript types) and minor transcript types (any of the rest of SO types in the list), with the implicit assumption that the first item in the list would be mRNA and the rest would be "something else."  The result looks like the attached screenshot, where the grey transcript is the non-coding one.

Here's what I'm wondering: is there any general interest in this addition?  I'm a few releases behind (1.11.6), so to properly give a pull request for these changes, I'd have to spend some time setting up a dev instance and testing that this additional is robust and sufficiently generic.

Thanks,
Scott


--
------------------------------------------------------------------------
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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