How To Create Mutation Diagram In R Or In Any Tools?
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8.5 years ago
henryvuong ▴ 800

Please let me know any tools or R packages that can create a mutation diagram showing mutations in protein domains like this figure from the MSKCC cBio Cancer Genomic Portal? Thanks in advance
enter image description here

mutation domain r • 32k views
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3
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Search your favorite search engine for "lollipop plot" or build your own, as described in another answer.

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5
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Thank all for the answers. Based on your suggestion, I found the R package MethVisual for visualization and exploratory statistical analysis of DNA methylation profiles by Arie Zackay and Christine Steinhoff. It will give me some direction to build my own code.

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Hi did you come up with something good? I looked at MethVisual, but it doesn't seem really straightforward to get to the cBio picture from there... Thanks if you can share some code!

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Please PM me your email. 

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I have been confused by the method of plotting mutations. Could you share your code with me? Thank you very much!

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I'm not aware of a specific package but I have made something very similar to this just using base graphics, i.e. rect, after moving the x-axis down with mgp, plot with type="h" for the vertical lines... it was quite straightforward.

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Could you share the code to do the same .

Thanks 

Saurabh

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Could you share the code to do the same

Thank U

Daniel

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Related post at StackOverflow:

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5.7 years ago
qiuworld.ou ▴ 130

Bioconductor package trackViewer gives beautiful lolliplot.

lolliplot trackViewer circle

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6.9 years ago
jeremy ▴ 110

Pfam provides an online tool to not only generate the domain information in JSON format, but to draw the lollipop diagram using javascript as well. They have more information here: http://pfam.xfam.org/help#tabview=tab9

IMHO, not as pretty as cBioPortal's but it gets you close to a solution.

EDIT / SHAMELESS PLUG: After seeing the data available and how easy it'd be, I made my own quick tool to fetch the data and draw the diagram for me in a style similar to cBioPortal - feel free to fork it and add features: https://github.com/pbnjay/lollipops

Example output (w/ labels per the comments)

TP53 w/ 2 mutations

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This is pretty badass.  Thanks! 

The only thing I wish it had was an option to show the mutation syntax provided on top of the lollies (perhaps at a 45 degree angle).

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Just pushed an update with the labels for ya - added an image to my answer above to show it off. 

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The tool is amazing. Thank you very much! Why the counts do not show up when I specifiy @2? it turns out the 45 degree angle only work for svg file but not for png, right?

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6.9 years ago
jeffk8900 ▴ 130

The cBIO portal team recently released a web based tool to generate lollipop diagrams.

http://www.cbioportal.org/public-portal/mutation_mapper.jsp

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The problem with mutation mapper is that the mutations are mapped to the longest transcript. Meaning that if you have a gene with multiple transcripts, the mapping to the domains of the shorter transcripts will be completely wrong!

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6.7 years ago
Michi ▴ 980

Hi

We found ourselves in the same need, we wanted such a plot (JavaScript). Thus, I add our solution, Mutations Needle Plot. The library creates an SVG image (with D3), which then may be downloaded.

You will npm in order to be able to install & run the library.

Examples may be found in the snippets folder or also the index.html - The one displayed here below

Mutation Needle Plot (muts-needle-pot)

 

 

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@Michi: is there a way to use snpEff VCF as input to generate mutations needle plot 

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Short answer, No. Long answer: Of course, but you would have to format the mutations a little bit :)

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6.9 years ago

My colleague @SolenaLS recently asked me to write something like this: (uniprot+SVG+javascript : ) http://lindenb.github.io/pages/uniprot/paintsvg.html

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5.5 years ago
zlskidmore ▴ 290

There's a developmental version of this type of diagram using R here, the function is called lolliplot.

Also in bioconductor devel branch. An example visual can be viewed from the vignette found here.

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Hi, do you know how to change protein framework by yourself rather than the default version from ensembl? Because I think the default version is too complicated and not simple and direct enough.

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5.7 years ago

Dear,

Colleagues have listed rectangular representations. I have recently published a circular version of such plots. Here is the website:

http://i-pv.org/

And here is an example:

http://i-pv.org/FOXP2.html

You can also search for I-PV for the posts in Biostar. 

I hope this helps,

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8.5 years ago
Pappu ★ 1.9k

Ensembl also gives similar plot

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