Plotting numbers of somatic substitutions per megabase (MB)
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5.7 years ago
rahel14350 ▴ 40

Dear Obi Griffith, Is there a way to plot the "Mutations per MB" in a separate plot not as a part of Waterfall using GeneVisR? Something like figure 1 in Alexandrov et al., 2016 https://d2ufo47lrtsv5s.cloudfront.net/content/sci/354/6312/618/F1.large.jpg Many thanks in advance, Rahel

GeneVisR Mutations per MB Waterfal snp exomSeq • 2.5k views
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If you are targeting this question at a specific Biostars user you could search for their user link under "community" ( e.g. your ID is https:// www.biostars.org/u/18508/ , a space added between // www to demonstrate what this ID looks like before it is automatically converted by Biostars code) and add that to your post.

This would "tag" that user and alert them that a question needs their attention.

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Are you supplying the Alexandrov example just to demonstrate layout? I ask because this figure has a lot more going on than just mutations/MB. It is showing mutations/MB brokend down by mutation type in several different ways. If that is what you want then it is a complicated question/answer.

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Dear Obi Griffith , Many thanks for your prompt reply. From this figure, I want to have the first part "Somatic substituion" per MB. I know that we can make a plot for mutations per MB in upper part of waterfall graph. But is that possible to make like this? I also have the mutation signatures using Maftools but that one also is not per MB.