Question: Music Proximity Analysis Mutation Diagrams
2
gravatar for joel.ferstay
6.3 years ago by
joel.ferstay20
joel.ferstay20 wrote:

I was just wondering if the MuSiC tool can generate diagrams like the Proximity analysis mutation diagrams shown in Figure 5 of the companion paper? Or were these generated by hand?

Thank you very much for your time.

music • 2.3k views
ADD COMMENTlink modified 5.2 years ago by Christian2.8k • written 6.3 years ago by joel.ferstay20
3
gravatar for Christian
5.2 years ago by
Christian2.8k
Cambridge, US
Christian2.8k wrote:

MuSiC lolliplots can now be created online at http://explorepcgp.org/proteinPainter.

ADD COMMENTlink written 5.2 years ago by Christian2.8k
1
gravatar for Cyriac Kandoth
6.3 years ago by
Cyriac Kandoth5.3k
Memorial Sloan Kettering, New York, USA
Cyriac Kandoth5.3k wrote:

We call those "lolliplots". :) They are generated with a tool that depends on our internal code-base and transcript-annotation data... making it very difficult to package as standalone tools like in the MuSiC suite. We do want to package it someday, but it's going to be a while. You can take a peek at the code on github, but be warned, it's non-trivial.

ADD COMMENTlink modified 6.2 years ago • written 6.3 years ago by Cyriac Kandoth5.3k

Just a follow-up question for how the lolliplot representation would treat data: I notice the lollipops "branch out" when there are variants in the same position sometimes, but in other instances the circle lollipops are stacked vertically when they occur at the same position.

Do they stack when the coordinate and type are exactly identical (recur across samples perhaps?), but branch when they are at the same position but of different type?

Thanks!

ADD REPLYlink written 6.2 years ago by joel.ferstay20
1

That's exactly correct. The same amino acid change stacks vertically. Different amino acid changes, even at the same position, branch outwards.

ADD REPLYlink written 6.2 years ago by ernfrid380

It's been four months since this post and I am wondering if in the meantime there became additional information available on how to produce such lolliplots? Is there maybe some kind of user manual?

ADD REPLYlink written 5.9 years ago by Christian2.8k
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