Is it possible to remove layers from anvi'o display?

[Hilary Morrison]

Oh experienced users--

I have refined my profile to a single large contig (587 splits) and no longer need to see the GC layer, taxonomy, etc. Can I hide or delete layers? And I'm NOT seeing ORF annotations in the inspect mode although I ran RAST. Any way to turn them on or re-incorporate the data or do I need to repeat the earlier steps?

Thanks,
Hilary

[A. Murat Eren]

Hi Hilary,

You can just put 0 for the "Height" attribute of any layer you want to remove (don't forget to save your state so you can load it later):

You don't need to re-run any of the earlier stages. If all you want to do is to put RAST output into your contigs database, you should be fine running this, and you will see all the ORFs the next time you run the interactive interface:

anvi-populate-genes-table -c CONTIGS.db -i svr_assign_to_dna_using_figfams.txt -p myrast_cmdline_dont_use

I hope these help!

--

A. Murat Eren (meren)
http://merenlab.org :: gpg

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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[hgm]

On Wednesday, December 30, 2015 at 12:09:58 PM UTC-5, Meren wrote:

Hi Hilary,

You can just put 0 for the "Height" attribute of any layer you want to remove (don't forget to save your state so you can load it later):

I thought this was the way to do it--will try again.  

[hgm]

Gene annotations--there are two cps genes annotated and they show up in the blue ring.  When I inspect those splits, I see the annotated gene in one and not the other.  And I think the RAST annotations were fine originally (I'm pretty sure I ran the step you suggested when I followed the tutorial) but I was not hovering the mouse in just the right way--or long enough. 

Thanks, Meren! 

 

[A. Murat Eren]

Hi Hilary,

How did you generate the file for the blue layer? Are you sure it is coming from the myRAST annotation? Because the inspect page *is* reading the genes from myRAST annotations, but the input for blue layer might be coming from elsewhere (i.e., RAST? (not myRAST)).

By the way, the 2.0 branch is a light-year away and much better than what you are using now. Here is how the genes look like in 2.0:

Windows instead of mouseover tips, and multiple sources for functional annotation...

I can't wait to release it.

Best,

--

A. Murat Eren (meren)
http://merenlab.org :: gpg

On Wed, Dec 30, 2015 at 1:54 PM, hgm <morr...@mbl.edu> wrote:

Gene annotations--there are two cps genes annotated and they show up in the blue ring.  When I inspect those splits, I see the annotated gene in one and not the other.  And I think the RAST annotations were fine originally (I'm pretty sure I ran the step you suggested when I followed the tutorial) but I was not hovering the mouse in just the right way--or long enough. 

Thanks, Meren! 

 

--

Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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[Hilary Morrison]

It's coming from the virulence gene search--"anvi-populate-search-table -c CONTIGS.db -H /workspace/shared/HMM_FOR_ANVIO/"

so apparently rast annotated one and not the other (?).

I *did* install version 2, but it doesn't seem to have taken...used the installer (new install, not update) but now I see that my dock icon is still 1.1.0 from October. I will try to uninstall old version and start over.

If I ever become anvi'o competent, you'll know that anyone can use it :).

> On Dec 30, 2015, at 3:08 PM, A. Murat Eren <a.mura...@gmail.com> wrote:
>
> Hi Hilary,
>
> How did you generate the file for the blue layer? Are you sure it is coming from the myRAST annotation? Because the inspect page *is* reading the genes from myRAST annotations, but the input for blue layer might be coming from elsewhere (i.e., RAST? (not myRAST)).
>
> By the way, the 2.0 branch is a light-year away and much better than what you are using now. Here is how the genes look like in 2.0:
>

> <image.png>

>
> Windows instead of mouseover tips, and multiple sources for functional annotation...
>
> I can't wait to release it.
>
>
> Best,
>
> --
>
> A. Murat Eren (meren)
> http://merenlab.org :: gpg
>
> On Wed, Dec 30, 2015 at 1:54 PM, hgm <morr...@mbl.edu> wrote:
> Gene annotations--there are two cps genes annotated and they show up in the blue ring. When I inspect those splits, I see the annotated gene in one and not the other. And I think the RAST annotations were fine originally (I'm pretty sure I ran the step you suggested when I followed the tutorial) but I was not hovering the mouse in just the right way--or long enough.
>
> Thanks, Meren!
>
>
> --
> Anvi'o Paper: https://peerj.com/articles/1319/
> Project Page: http://merenlab.org/projects/anvio/
> Code Repository: https://github.com/meren/anvio
> ---
> You received this message because you are subscribed to the Google Groups "Anvi'o" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to anvio+un...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/anvio/5949fb76-1792-48e0-a05f-3e52d1e65a83%40googlegroups.com.
>
> For more options, visit https://groups.google.com/d/optout.
>
>
> --
> Anvi'o Paper: https://peerj.com/articles/1319/
> Project Page: http://merenlab.org/projects/anvio/
> Code Repository: https://github.com/meren/anvio
> ---

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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Hilary G. Morrison, Ph.D.
Senior Research Scientist
Josephine Bay Paul Center
Marine Biological Laboratory
7 MBL Street
Woods Hole, MA 02543-1015

508-289-7339

[A. Murat Eren]

Now it is more clear! Yes, when you run this:

anvi-populate-search-table -c CONTIGS.db -H /workspace/shared/HMM_FOR_ANVIO/"

It stores the HMM hits to the profile in that directory --which is completely independent of RAST or myRAST annotation. Hence, it is not surprising to not see the gene identified by HMM as annotated by RAST also in inspection.

2.0 branch needs a bit more time :) So you can wait a little longer maybe!

I am very glad you are playing with anvi'o, and making progress with it!

Best,

--

A. Murat Eren (meren)
http://merenlab.org :: gpg

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