Reconstruct principal curves from the results of pathifier package

Question

[arronar]

Hello.

I'm using the pathifier tool, to extract PDSs (Pathway de-regulation scores) from some microarray datasets. If someone has already read the paper of this tool, probably he/she has seen the following image of the constructed principal curves.

I search on the internet for a tutorial on how to construct such plots from the results of pathifier, but couldn't find something. As you might know the quantify_pathways_deregulation() returns a curves list but I don't know exactly how to use it.

Does anyone try to re-construct such curve plots from pathifier's results?

Any hint or idea is welcome.

Answer 1

[Suren]

Check here .

They shared R codes to do exactly the same. You can also use the produced *RData files to extract the data for constructing the principal curve using scatterplot3d package.