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Topic: Visualize samples' abundances as pie charts on Cytoscape. (Read 2359 times) previous topic - next topic

Visualize samples' abundances as pie charts on Cytoscape.

Hello everyone!
I use MSDial ver 4.20 to process data from 8 different samples together. After exporting the mgf file and using the GNPS platform to construct the Molecular Network, I open the MN on Cytoscape_3.8.0
The problem is when I try to visualize samples' abundances as pie charts on Cytoscape. Even when I give different names for the samples on a metadata file, I do not find the name of the samples as group options to color them separately. It appears that the MSDial mixes data from all the samples at alignment result and do not allow the users to access the sample of origin of each spectrum.
Is there a way to color the nodes according to the samples of origin after processing data with MSDial?

Re: Visualize samples' abundances as pie charts on Cytoscape.

Reply #1
Hi,
Thanks for using the feature-based molecular network method on GNPS ! Please make sure you are following recommendations in the documentation at https://ccms-ucsd.github.io/GNPSDocumentation/featurebasedmolecularnetworking-with-ms-dial/

Note that for MS-DIAL's metadata in GNPS molecular networks visualized with Cytoscape, the following is required:
"IMPORTANT WHEN USING A METADATA TABLE WITH MS-DIAL: "filename" in the metadata files for FBMN with MS-DIAL should not contain file extensions (ex: "sample1.mzML" must be "sample1")."

If you need more support, please use the GNPS forum and provide the GNPS job link.
https://groups.google.com/forum/#!forum/molecular_networking_bug_reports

Cheers,

Louis-Felix