Announcement

Collapse

Welcome to the New Seqanswers!

Welcome to the new Seqanswers! We'd love your feedback, please post any you have to this topic: New Seqanswers Feedback.
See more
See less

Mutation cluster plot

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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

  • #2
    I guessed people just made them in powerpoint, but if there is such a tool, I'd be very interested.

    Comment


    • #3
      I don't think so, Rock. Let's wait for other's comment as well.

      Comment


      • #4
        Did you try to contact the corresponding author from the Nature paper that contained the figure in question?

        Comment


        • #5
          Not yet, I think I should try that.

          Comment


          • #6
            Any response?

            Comment


            • #7
              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, 05:45 AM. Reason: stil cant spel

              Comment


              • #8
                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.

                Comment


                • #9
                  Hi, pravee1216, have you found the method that got such mutation plot? If did, could you give me some information? thank you!
                  Lee

                  Comment


                  • #10
                    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, 08:41 AM.

                    Comment


                    • #11
                      Thank you! It is very useful!

                      Comment

                      Working...
                      X