Abstract
This script can be used to automate the annotation of a molecular network and visualization thereof in CytoScape. The current version of the script uses a .graphml file generated by GNPS (version 1) as input, processes the node and edge table, and creates various visual style mappings to make the molecular network more informative. Molecular networks from other sources can be used, but it is likely that column names used in this script to reference the node and edge table will need to be modified. The visual styling that is applied by this script adds compound names and precursor mass as node label, scales node size based on log2 total precursor abundance, adds color to edges to differentiate between ion identity molecular networking edges and cosine similarity edges, scales edge width to show strength of associations, colors nodes based on groupings, and adds pie charts and molecule structures onto nodes. To run this script the CytoScape software should be running on your device, so RCy3 can communicate with this software. In addition, the following app should be installed in CytoScape to make the drawing of molecular structures possible: https://apps.cytoscape.org/apps/chemViz2.
Example input data and expected output data are included.
Example input data and expected output data are included.
Original language | English |
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Publisher | Wageningen University & Research |
Media of output | Online |
DOIs | |
Publication status | Published - 17 Jul 2024 |