MutationMapper on local server

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Cyril Fournier

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Jul 13, 2021, 11:43:03 AMJul 13
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Dear cBioPortal team,

I would like to know if there is a way to use your Mutation Mapper tool locally on a server ?
It would be fantastic if I could integrate the creation of such plots with my own data to my routine pipeline, working on a CentOS 7 server. I see that we can request your database via R, but I can't find any help about using MutationMapper via your R library.

Wish you a great day,
Best regards, 

Cyril Fournier

Ingénieur Hospitalier - Bioinformaticien
Service Epigénétique Oncogénétique 6255
Équipe IGEO
Dijon University Hosiptal,
INSERM 1231,
University of Burgundy, France

Bâtiment B3 - bureau R36
15 Boulevard Maréchal de Lattre de Tassigny,
21070 Dijon Cedex
cyril.f...@u-bourgogne.fr

lisman...@gmail.com

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Jul 14, 2021, 10:15:10 AMJul 14
to cBioPortal for Cancer Genomics Discussion Group
Hi Cyril, 

I'm consulting with my team about the best way to do this. 

Aaron Lisman

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Jul 14, 2021, 10:30:15 AMJul 14
to cBioPortal for Cancer Genomics Discussion Group
Hi Cyril, 

So, we could quite easily adapt the mutation mapper page (https://www.cbioportal.org/mutation_mapper) to accept posted data (HTTP POST).  So, in R, you would assemble the mutation data and then script to open a browser window with a post request.   This assumes you have a human user who just wants to see the generated visualization and perhaps export it.   If you actually want to be able to spit out a bunch of SVG or PNG files automatically, probably the easiest thing to do would be to use a headless browser automation tool (e.g. https://github.com/puppeteer/puppeteer) to do automate the interaction with the browser on a server (and save exported file somewhere).    This would still necessitate the work on our end to accept posted data. 

So, let us know what your desired use case is.

--Aaron







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