Output format / metadata

NPLinker / nplinker

A python framework for data mining microbial natural products by integrating genomics and metabolomics data

https://nplinker.github.io/nplinker

Apache License 2.0

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Output format / metadata #11

Open andrewramsay opened 5 years ago

andrewramsay commented 5 years ago

what kind of output (and in what format) should we provide the user. Simon's initial thought would be that for any pair of GCF and Spectrum (or group of spectra, see #10) we will have a number of scores, some of which can be considered significant. This could be output in a form that could be loaded into Cytoscape where significant scores form edges between GCF and spectrum / spectral group objects? Open to suggestions here, and I’m sure Justin’s input would be valuable.

florian-huber commented 5 years ago

I just made a pull request with an extended and updated version of my data_linking classes and functions. This also contains a new function to create a network from selected links (based on a score of choice). This network is then exported as graphml file which can be imported in cytoscape.

What's still missing is the export of additional annotations. That will be done next...