Question: Clonal Evolution Plot (figure 3d)
1
gravatar for david.melnekoff
11 months ago by
david.melnekoff10 wrote:

Hello,

I'm having difficulty finding any information about how figure 3d, the schematic showing Clonal Evolution, was generated. Any information would be greatly appreciated!

Thanks -David

sciclone • 902 views
ADD COMMENTlink modified 11 months ago by Chris Miller18k • written 11 months ago by david.melnekoff10

Where can one find that figure 3d?

ADD REPLYlink written 11 months ago by genomax226k

in the sciclone PLOS paper

ADD REPLYlink written 11 months ago by david.melnekoff10
1

You had better provide a link in your original post since people (including me) are not going to go searching for it.

ADD REPLYlink written 11 months ago by genomax226k
4
gravatar for Chris Miller
11 months ago by
Chris Miller18k
Washington University in St. Louis, MO
Chris Miller18k wrote:

You're referring to the plot in Figure 3d here: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003665

That was hand-generated in Illustrator, but you have fortuitous timing. I'm just wrapping up an R package to generate those plots: https://github.com/chrisamiller/fishplot

enter image description here

Give it a try, and I'd welcome feedback on that early release.

ADD COMMENTlink written 11 months ago by Chris Miller18k
1

Great timing on @david's part indeed.
And you saved him the effort of pasting a link to the paper as well.

ADD REPLYlink written 11 months ago by genomax226k

Great! I'll give it a try and let you know.

ADD REPLYlink written 11 months ago by david.melnekoff10

Hi Chris I have one more question. Does Sciclone output tumor fraction of clones in any indirect or direct way? Or is it as simple as : # of variants in cluster one, over total number of clustered variants would give clonal fraction of clone#1?

Thanks again, David

ADD REPLYlink written 11 months ago by david.melnekoff10

I'd recommend feeding the sciclone results into clonevol, which will infer phylogeny and give clonal fractions. https://github.com/hdng/clonevol

ADD REPLYlink written 11 months ago by Chris Miller18k

I am using Clonevol, and it is giving me two or more models for the same patient, for example one with model probability of 0.49 and one with model probability 0.47. I only have two samples per patient. How to you choose the model when it gives several possible models. Is it enough to choose the one with the highest probability?

ADD REPLYlink written 6 months ago by chloe.steen120

If there are two models with high probability, then it means there's not enough information in the data to distinguish between the two. There's likely nothing you can do without getting more data (in the form of another sample that's spatially or temporally distinct)

ADD REPLYlink written 6 months ago by Chris Miller18k
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