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Old 03-20-2012, 08:30 AM   #1
pravee1216
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Default Mutation cluster plot

Just a quick question. Does anyone has any idea which tool can produce this kind of plot for NGS mutation data. This is really a great representation of missense/indels at protein sites with mutation changes of a particular gene.



Above pic is from a nature publication, but I have no idea which tool was used for plotting the mutations.

Thanks in advance for any help.

Raj
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Old 03-21-2012, 04:45 AM   #2
RockChalkJayhawk
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I guessed people just made them in powerpoint, but if there is such a tool, I'd be very interested.
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Old 03-21-2012, 09:20 AM   #3
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I don't think so, Rock. Let's wait for other's comment as well.
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Old 03-21-2012, 12:20 PM   #4
HESmith
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Did you try to contact the corresponding author from the Nature paper that contained the figure in question?
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Old 03-22-2012, 09:05 AM   #5
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Not yet, I think I should try that.
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Old 06-06-2012, 03:35 AM   #6
RockChalkJayhawk
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Any response?
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Old 06-06-2012, 03:51 AM   #7
Richard Finney
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There's likely an artist on staff at the institution whose scientists are producing the paper. I'm guessing it's "hand drawn" using an SVG editing tool or Photoshop. It's become de rigueur for Nature level publications. The prototype components might be coming from a graphic produced by R. It takes a lot of practice to get good with an artist's tool and a lot of patience to get the scientific details. An "all thumbs" scientist might want figure out who the local graphics guru is.

Last edited by Richard Finney; 06-06-2012 at 05:45 AM. Reason: stil cant spel
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Old 06-07-2012, 09:04 AM   #8
pravee1216
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I contacted the team who published the nature publication. They used an in-house tool to produce these plots. They're in the process of publishing it, hence under manuscript review. Meantime, I asked my team to look into this as I plan to integrate many more information on the same plot.
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Old 05-13-2014, 04:43 AM   #9
lipeiqiang
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Hi, pravee1216, have you found the method that got such mutation plot? If did, could you give me some information? thank you!
Lee
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Old 05-14-2014, 08:32 AM   #10
m_two
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These lolliplots/mutation diagrams required minimal touch up:
http://www.nature.com/ncomms/2014/14...ms4156_F3.html

They originated from:
https://github.com/genome/gms-core/b...tionDiagram.pm

The code has some internal dependencies.

Check out:
http://explorepcgp.org/proteinPainter
http://bio.ieo.eu/fancygene/

Also related:

https://www.biostars.org/p/80406/
https://www.biostars.org/p/68778/
http://www.biostars.org/p/18117/
http://www.biostars.org/p/45397/

Last edited by m_two; 05-14-2014 at 08:41 AM.
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Old 05-14-2014, 08:39 AM   #11
lipeiqiang
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Thank you! It is very useful!
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