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CCMS-UCSD / GNPSDocumentation

Documentation for GNPS and related tools as written in mkdocs
https://ccms-ucsd.github.io/GNPSDocumentation/
MIT License
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GC-MS | features missing in the cytoscape file #316

Open MelissaESPOSITO opened 3 years ago

MelissaESPOSITO commented 3 years ago

There are missing features in the Cytoscape file. https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=ea8bae87c7f244508f151a5a57f66e15 features that are in my aligned table (from MZmineADAP) are missing in the Cytoscape but are in the GNPS job at "view all spectral libraries" the example of feature 76 is illustrated in the following picture: F1 F2

MelissaESPOSITO commented 3 years ago

From the 539 features that I have in the aligned table and the mgf, only 366 are in Cytoscape. Are the 173 missing features single nodes so not in the network?

MelissaESPOSITO commented 3 years ago

Picture1

lfnothias commented 3 years ago

Is there any single nodes in the Cytoscape file ?

MelissaESPOSITO commented 3 years ago

with MS-Hub https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=0412c4419679484790992a65bc44211b https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=9c692c2a4d0c4fab94b21094516c1020 with MZmine https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=ea8bae87c7f244508f151a5a57f66e15 https://gnps.ucsd.edu/ProteoSAFe/status.jsp?task=6a56f3f854e8434da30bb7613ee49343

MelissaESPOSITO commented 3 years ago

no, there is no single nodes in the Cytoscape file

lfnothias commented 3 years ago

Then it is likely the reason. @mwang87 would that be reasonable to add an extra graphml file containing the single nodes ? Or something else would be best suited ?

mwang87 commented 3 years ago

Sorry to be late on the follow up, seems reasonable to add singletons into the graphml. we could add another file like we do for classic networking.