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Reconstruct principal curves from the results of pathifier package

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.

enter image description here

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.

pathway pathifier principal curves bioconductor r
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updated by Suren Suren • written by arronar arronar

1 answer

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.

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written by Suren Suren

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